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 today's world.  All sorts of things can evolve, so this may be the feature of Life found most often in things that are not alive.  Evolution also acts on populations - what changes is the "average individual" in a diverse population.

Of course, for a long time it wasn't known that Nature had ever been any different than it is today - people accepted historical changes in cultures and societies, but not in the types of living things.  For a long time, they had no reason to think that the world had not always been just like the world they knew.  At the birth of modern western science during the Renaissance, it was still widely accepted that the Earth was only a few thousand years old, and Nature was a continuation of the Perfect Creation of Eden - only Man, with his ability to choose, was a flawed product of the Garden.  However, during this period a systematic approach was taken to studying fossils, and it was quickly found that the deeper (and older) a layer one looked at, the less like modern forms the fossilized animals were (animal hard parts fossilize much better than plants, and plant evolution is less dramatic than animal evolution).  In very old layers, there were types that seemed almost totally unlike anything existing today, such as the dinosaurs.  In newer layers, there seemed a progression of types that became more and more similar to things living today.  Attempts to explain fossils away as some sort of bizarre rock formations found some acceptance, and worked all right for separate bones, but it became impossible to explain toothy skulls and near-complete skeletons that way.

Most fossil beds contain the remnants of creatures from the sea floor, since most fossil layers are sedimentary rock that at one time were sediment layers under a body of water.  One of the first men to study such formations, Charles Lyell, became one of the most powerful influences on both geology and biology.  He decided that the production of fossil beds and the nature of the fossils themselves suggested a long, continuous process in a world that worked pretty much the same way as the world we see around us today (this idea, which didn't originate with Lyell but was not widely-accepted before his publications of the 1830's, is called uniformitarianism);  he calculated layer ages based on how sediments deposit now, and he rejected the idea of abrupt changes (and so rejected those who connected hundreds of meters of sedimentary rock to deposits of the Biblical flood) or that the physical processes of the ancient world were significantly different than today.  He was also one of the first widely-accepted voices to reject a Young Earth, as there was too much sediment accumulation shown in the rocks (even ignoring compression) to have been done in a few thousand years.  His calculations for the actual age of the Earth increased throughout his life as more information came in - by his death, he felt that the earth was several hundred million years old, and it is now thought that the Earth is 4 to 5 billion years old.

Two concepts arose that challenged the Word of the Bible and were considered blasphemous in those times.  The first we might hardly realize was ever controversial:  extinction.  Fossils indicated the disappearance of many past species, but fundamentalist reading of Scripture declared the Bible to be totally incompatible with the idea that one of God's creations could simply die out; that idea has since been universally accepted.  Some Biblical scholars suggested  that Man's world is not the first Creation, and fossils are remnants of earlier versions, but this way of reading the text never really caught on.

The second concept is evolution, the idea that types of living things have changed over time, that modern forms are significantly different from their distant ancestors, and that ongoing influences in Nature produce continuing change.  This idea is not totally incompatible with religious ideas, and in fact is accepted widely by people whose religious texts might seem to say otherwise, but there are many who choose to resist the idea.  Evolution, many have decided, represents a sort of "progressive Creation" which is all still part of God's Plan for the world.  

In evolution, the underlying assumption that human beings must have evolved from non-human ancestors that produces the biggest "sticking point," which is understandable.  Humans are strongly invested in the idea that they are somehow special and exist apart from the rest of the living world, and most evolutionary concepts challenge that assumption.  However, it should not be assumed that biologists are mostly atheists, as they are not.  As humans are expert at, they usually adjust their religious concepts to fit with the realities of their particular worlds.

Once the idea of evolution gained some momentum, the question of how such a process works became very important.  Many prominent naturalists came up with various explanations, but only a few are still widely remembered.

Lamarck.  Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck is known to history as a Man With a Silly Idea, which is unfair.  Strangely enough, during his life his ideas were largely ignored by his peers, but became influential long after his 1829 death.  Two concepts that are associated with Lamarck, neither true, are:

Evolution by Inheritance of Acquired Characteristics. Lamarck grasped that inherited changes, influenced by the environment, were important to evolution, and he wasn't wrong.  His mistake was in believing that changes in features developed during a lifetime (say, weightlifting to make yourself more muscular) could be passed to offspring (the children would themselves be born more muscular).  He thought that an organism's active adaptations to their environment could be passed on.  But would you be surprised if a world-class bodybuilder's children were more muscular than most kids?  What we now accept is that something about that bodybuilder's genes, something that gave them the potential to train and to be more muscular than most, could be passed on, but genes were unknown in Lamarck's time, and what seemed logical then no longer seems so now.  What should also be noted is that Lamarck seemed on the same track that Darwin later wound up on in explaining evolution:  how traits that were well-adapted to the environment would be passed on and produce longterm changes.  He just was wrong about how traits got passed on.

Evolution = Improvement.  A typical philosophical approach for scientists of the 1800's was to hypothesize as a way to investigate and describe the Perfection of God's Creation.  Much of Renaissance science was in fact funded by the Church, where it had been decided that understanding Nature was part of Man's purpose.  Part of the idea is that Modern Man, and the world he lives in, is the culmination of that divine plan, and so all evolution is a pathway, onward and upward, to that goal.  This idea, that evolution is a process of betterment working toward some goal of perfection, still has a strong influence on how people, even biologists, see evolution, although the widely-accepted idea is that evolution is a generation-to-generation adaptation to current conditions, which change randomly and over time and produce random evolutionary pathways.

Thomas Malthus.  In the early 1800s, Malthus developed his ideas about how conditions affect populations.  He talked about the Natural world, where the rate at which a population could increase was exponential while resources remained about the same; populations would therefore be limited by disease, famine, and conflict, but there was a warning embedded about growing human populations as well (and maybe suggestions on how to use the principles to limit the numbers in the lower classes).  These ideas were huge influences on the evolutionary theories of both Lamarck and Darwin, who both talked about environmental influences on groups as a basis for evolution.

That idea, the current best explanation for how evolution works, is the Theory of Evolution by Natural Selection, developed and written down originally by Charles Darwin and Alfred Russel Wallace in 1858, with many slight 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.

Charles Darwin.  Product of a fairly well-to-do but largely dysfunctional family, Darwin resisted his father's ideas of what sort of career he should have, and in 1831 took a position on the exploratory ship HMS Beagle, more or less to give the Captain someone of the same "station" for company (the social isolation of captains over long voyages had become quite a problem).  Darwin also took on the duties of the Ship's Naturalist, and went on a voyage around the world, with notable stops along the coast and islands of South America.  Because of horrendous seasickness (and possibly personality clashes with the Captain), Darwin spent as much time as possible ashore, collecting samples and taking notes and making observations.  One thing he noticed was that the character of the animals and plants on islands resembled, or didn't, those of other islands nearby and the mainland, dependent upon how close together they were and how much the physical nature of the environments differed.  The strangest collections of creatures by far were found by Darwin on the Galapagos Islands, a collection of arid islands some 1000 kilometers from the equatorial jungles of South America.  The limited types of animals there had obvious relatives on the mainland, but were different species particularly suited to the different lives available on the islands.  Assuming that their ancestors were groups of mainland animals unlucky enough to wind up there, how did they evolve into these different species?  During his travels, Darwin began to develop his explanation for just such processes, which he came to call Evolution by Natural Selection.

What is Evolution by Natural Selection?  Sometimes nicknamed "Survival of the Fittest," it would be more appropriate to call it "Reproduction by those Fit best."  Simply put, in any given group of organisms, there will be some variety of features that directly affect how good the chance is of each individual living to reproductive age and then successfully reproducing - as a general trend, each generation of offspring will, more and more, reflect features that were advantageous to their parents, grandparents, etc.  Fitness actually means how well something "fits."  The important detail here is that environments change over time - and what was a good feature in one time and/or place may not be elsewhere - and these changes in environment (the "Nature" part of Natural Selection) influence (the "Selection" part) which individuals survive and reproduce and what useful 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, has changed so significantly from the "type" of its ancestors that it needs to be relabeled.

Darwin was strongly influenced by some knowledge of animal husbandry - he knew that breeds of domestic animals could be changed over time by selecting which individuals breed, a process that has come to be called artificial selection.  In Natural Selection, the "picking" of the breeders is dependent on which individuals can survive and succeed under the conditions around them.

Evolution is not an "ever upward movement toward perfection," as Lamarck and many of his time believed;  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, and not everything evolves at the same rate, partly because the rate depends both on how fast the environment changes, which varies considerably from place to place (and even pieces within environments vary), and on the rate of reproductive "turnover" that can give short-lived organisms much faster potential rates than long-lived ones.   Also, the trait variations selected are whatever is there in the population at the time;  populations don't get what they need (something Lamarck believed, as part of the "plan"), selection just works on what's there.  This means that variation within a population is an important basis for its evolutionary potential.

When Darwin returned to England, he settled into a role as a naturalist and went about writing up his theories, although he seemed in no hurry to actually publish them.  He made his reputation as an expert on smaller topics, such as earthworms, and certainly seemed comfortable discussing his ideas with other naturalists.  It's likely he knew what sort of reaction a widespread distribution of his theory would get from the general public.

Then, along came Alfred Russel Wallace, whose travels through South America (where virtually his entire specimen collection was destroyed in a shipwreck) and Indonesia (perhaps the world's largest collection of islands, presenting huge numbers of separate- but- somewhat- connected environments) led him to essentially the same ideas that Darwin had come up with.  In the late 1850's, Wallace wrote an article based upon his ideas and sent it off to England, where it was brought to Darwin's attention (some accounts have him sending it through Darwin, but that seems unlikely).  Once published, the concepts would from then on have been linked only to Wallace;  Darwin arranged it so that when Wallace's paper was made public, it was accompanied by a similar one by Darwin.  They brought out the same idea "simultaneously."

In the years that followed, Charles Darwin became much more associated with Evolution by Natural Selection than Wallace.  There are many reasons for this:  Darwin was in England, where he had an established reputation, while Wallace, who would not return from Indonesia for a few years, was less well-known or respected.  Also, Darwin's ideas were soon presented in a book, On the Origin of Species, which was widely-read and became the particular reference source on the subject.

Darwin also developed a theory of Evolution by Sexual Selection to explain traits that had obvious advantages in the competition for mates but which might actually be disadvantages from a survival standpoint, traits such as a peacock's tail.  This was not difficult to integrate into his ideas, since it is actually reproductive success that ultimately decides which traits get passed on and affect the nature of descendants.  Evolution may be a balance between what helps you survive long enough to reproduce and what helps you actually accomplish the reproduction.  And, in an example of an established term broadening into a confusing area, "sexual selection" can be applied to any feature that aids reproduction success, even in asexual reproducers.

Not surprisingly, Darwin's ideas were controversial and remain so to this day.  What also shouldn't be surprising is that, although the idea of natural selection has great explanatory power for evolution, there are parts that Darwin couldn't explain because no one knew how certain processes work.  Like any great, descriptive theory, the years since its release have seen a long procession of tinkerers that have adjusted it here and there.  As we continue through the history of biology, we will investigate the impact of later developments.

One side-note to the theory:  the French translation of On the Origin of Species tended to include "interpretations," including a subtitle, that suggested that the whole idea confirmed Lamarck's ideas.  Even the word "selection" was replaced with the word "election," implying more purpose and plan.  That version was used widely in Europe;  its difficult to assess how that affected later developments there.

Although fossils were some of the first aspects of nature whose explanation led to ideas of evolution, they have limited use in providing evidence for the theories.

As said before, fossils are usually found in layers of sedimentary rocks, from newer surface rocks to older deep layers.  The organisms died and sank to the bottom, where usually their soft parts were consumed (and often hard parts scattered) by other organisms and only shells, bones, and teeth remained.  And for large organisms, even those that lived in water would be few and far between in the sediments (think about trying to find a shark carcass on the bottom), so it's amazing that there are many fossils of big land animals (like dinosaurs) at all!

These ancient layers of sediment were laid down in bodies of water, but most known fossil beds are no longer under water (the major dinosaur beds of North America haven't been under water for tens of millions of years).  So the record in any given place usually has time gaps of varied width, occurring at varied points in history when that land has risen above sea level or inland bodies have dried up.  Fossils can also be made when organisms are covered by sand, or tar (a rare happening), or pine sap (amber fossils), or volcanic ash (but not lava - lava tends to be too destructive and produce too hard a rock to be good for fossil finding) - fossil footprints often were made in wet sand that was covered by ash that dried and protected them.  Objects in the buried layers lose water and accumulate minerals, eventually becoming petrified, or rock-like - becoming fossils.

So what's in the fossil record?  Mostly small ocean-living shelled animals, such as clams and snails.  The evolutionary record for these creatures is especially good, but of little interest to most people who want to see a progression of forms in the larger, sexier beasts, for which fewer fossils exist.  We may have a single individual for a wide span of time, and no way to know how typical it was or really how linked to an evolutionary sequence it may be.  Those who criticize evolution often use the "spotty" fossil record for their evidence, and it's easy to see why.

Through Darwin's time, most of the time relationships between types of organisms were determined using comparative anatomy, as discussed earlier, relating homologous features between living forms and between fossils and living forms.   When homologous features become used for different purposes - are no longer analogous - the process is called divergent evolution, the splitting of a family tree in different functional directions.  When unrelated groups have analogous but nonhomologous features (wings in birds and butterflies, fins in squids and seals), the process is called convergent evolution (sometimes parallel evolution) - similar needs may produce superficially similar structures, even if they're built on different underlying architecture.

With the development of the microscope, this could be extended to microscopic anatomy:  features could be compared on the level of the tiny, as well.  And later, comparisons could be made on molecular sequences, such as the sequences in proteins or DNA.  

One type of early comparison was championed by Ernst Haeckel in the late 1800's:  looking for similarities between the embryo forms of animals, specifically in backboned animals (vertebrates).  Relating the progression in form of developing mammal embryos to the progression of forms in the fossil record (fish to amphibian to reptile to mammal), Haeckel claimed that "Ontogeny recapitulates phylogeny," or that we "replay" our evolutionary history as embryos, going through a fish, then an amphibian, then a reptilian form on our way to being mammals.  This theory was a product of real similarities, enhanced by Haeckel's sincere belief that they existed (science truism - we often see just what we expect to see, even if it isn't really there), but it turned out to not really be true.   We may have some fishlike structures in early development, but we aren't actually fish at that stage.

But comparing embryos is very important, because evolutionary changes rarely impact early development.  For one, the "environment" of embryos (such as the inside of an egg) may be much more similar than the broader environment around it, so selection on embryos is minimal.  Also, the earlier that changes occur during development, the larger (and more likely not good) the impact can be, and evolution tends work more by small variations than huge leaps.  This means that organisms that don't look at all related as adults can be "connected" by finding embryo similarities "left over" from their shared distant ancestors.  It tells us that humans are more closely related to starfish than they are to clams, for instance, which would seem hard to determine looking at adults.

Some of the most widespread connections have come recently, as researchers have looked into the genes responsible for very early embryo development.  These homeogenes or hox genes code for proteins that determine front-and-back, right-and-left, inside-from-outside-layers, organ placement, and so one, and are turning out to be remarkably similar across wide ranges of organism.  For example, almost the same exact gene determines eye placement in both fruit flies and mice.  This makes sense, since basic layout genes could be used to produce a wide range of organisms.  And they do.

Other genetic-based revisions of evolutionary theory will be covered in the genetics chapter.

How fast does evolution move along?  Darwin, with his background in uniformitarianism, thought it a long, slow, gradual process.  Evidence from the fossil record (such as it is) seems to indicate a punctuated process - long periods during which things barely change, and then quick transitions to new forms.  These ideas once produced two "warring camps" in evolutionary biology.  We know now, like most of the times such battles arise, the truth is a combination of both.

According to the theory of Evolution by Natural Selection, evolution is tied to the environment, and we know that environmental change is sometimes slow and gradual and sometimes quite fast between relatively stable but different eras.  Why wouldn't evolutionary rates reflect that?

In some ecosystems or parts of ecosystems, changes almost never happen.  For instance, there have been beach ecosystems and open, deep-water ecosystems since before there were animals to occupy niches in them;  they just haven't always stayed in the same places.  Some species long ago adapted well to such systems and have moved with them as the systems have migrated;  being in a stable environment, these species have also shown very little change over a very long timeframe.  Beach system-inhabiting horseshoe crabs today look almost exactly like their 100-million-year-old fossil relatives.  Large open-water sharks have almost as long an unchanged history.  In fact, it has been found that such animals are particularly resistant to mutations, one of the bases for evolutionary change (thats why sharks rarely get cancer, commonly a product of mutation - it's not the "magic" cartilage).  These organisms have actually evolved a resistance to evolution!

Another important part of evolution is that it is driven by reproduction over multiple generations, which means that a species that reproduces very rapidly can also evolve very rapidly (depending upon reproduction type and variability within each generation).  In the evolution of diseases, when small, quick-reproducing organisms invade larger, slower-reproducing ones, each evolves, but the "germs" tend to evolve / adapt faster. 

The idea that all living things, including humans, evolve, challenges many cultural and religious beliefs about the position and uniqueness of Man in the world.  This, of course, was among many such challenges that arose as Man learned more about how Nature works, and eventually, ideas about the flatness and centrality of the Earth, the extinction of created types, and many others have shifted from blasphemous to widely-accepted.  But evolution, which can be seen at work in many subtle ways, as an idea hasn't the blunt force support of something like a round or revolving Earth, and can still be denied.  And denial is fine, but this has become more like a battle between things that really can't fight.  In opposition to the concept of evolution are articles of pure faith, which are either factually unsupportable or scientifically untestable.  And shouldn't such faith-based things be untestable?

In the battle that does wage, however, the concepts of evolution are usually misrepresented.  One hears that evolution is "controversial," and filled with "dissenting opinions."  However, evolutionary theory is the supporting idea of biology the way that atomic theory supports chemistry or gravitational theory supports astronomy:  there's no real doubt that everything is driven by such forces, and although scientists may disagree on the details of how the forces work, the concepts have as much weight as anything is allowed to have in science.

Somehow, since evolution seems to conflict with a particular interpretation of some religious treatises, this has led to a portrayal of science as being faithless, as if all scientists were atheists, which is of course untrue.  Religious scientists tend to have beliefs that are not literal fundamentalism, but that tends to be true with highly educated people in general;  that doesn't make them somehow less spiritual than literalists.  Evolution has also become a political issue, as if it was by definition anti-religion, when it surely isn't.  A person's appreciation of how the world works, with whatever driving force they believe, is enhanced by learning the rules - Darwin, Wallace, and Lamarck were trying to gain insight into God's role in their world by working out the Rules of Existence.
 

Everything You Might Want to Know about Charles Darwin -  The Darwin Page.

A transcript from an interview with a Christian biologist.

A paper on the stepwise evolution of the bacterial flagellum, often presented by Intelligent Design advocates as a system that could not have evolved in useful stages, but must have appeared fully-formed.

Darwin rap-?