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.  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 present-day Nature was a continuation of the Perfect Creation of Eden - only Man, with his ability to choose and a history of choosing badly, was flawed.  Then fossils, which had been known and collected for millennia but apparently not analyzed much, became a subject of study.  But how could these be the remains of ancient animals?  When they were analyzed, attempts to explain fossils away as some sort of bizarre rock formations found some acceptance, and it worked all right for separate bones, but it became impossible to explain near-complete skeletons that way.  As with many other aspects of the natural world, 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.  

Most fossil beds contain the remnants of creatures from the sea floor, since most fossil layers are sedimentary rock that at one time was sediment in 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 in history.  He decided that the production of fossil beds and the nature of the fossils themselves suggested a long, continuous process in a world not very different from what we see around us today (this idea, known before Lyell but not widely accepted until his publications of the 1830s, is called uniformitarianism);  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 major differences in conditions in ancient times.  He was also one of the first widely-accepted voices to reject a Young Earth, as there was too much sediment accumulation to have been produced in just 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.  The first we might hardly recognize as a problem today:  extinction.  Fundamentalist reading of Scripture led to certainty that one of God's creations could not simply die out.  Eventually this idea, like the earlier certainty that the sun moves around the earth, stopped being an issue.  Some Biblical scholars still ascribe to the idea that Man's world is not the first Creation, and fossils are remnants of earlier versions, but this idea is not widely accepted anymore either.

The second concept is evolution, the idea that types of living things change 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 seem to say otherwise, but there are many who choose to resist the idea.  Many religious people look on evolution as a sort of "progressive Creation" which is all still part of God's Plan for the world.  

In evolution, it seems to be that the underlying assumption that human beings 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 belief.  However, it should not be assumed that biologists are mostly atheists, as they are often portrayed.  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, his ideas were largely ignored by his peers, and were influential mostly 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 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, that something about that bodybuilder's genes gave them the potential to be special and could be passed on, was 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 wound up on in explaining evolution:  how traits adapted to the environment would be passed on and produce longterm changes.  He just was wrong about how traits got passed on.  Darwin incorporated some of these now-abondoned ideas into his own theories, but they were not critical to the overall concepts and are ignored today.

Evolution = Improvement.  A typical philosophical approach for scientists of the 1800s was to hypothesize as a way to investigate and describe the Perfection of God's Creation.  This was a natural scientist's job!  Part of the idea is that Modern Man, and the world he lives in, is the culmination of a 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 produce random evolutionary pathways.  "Better" is very much a relative term - what was better during the Ice Ages is not necessarily better today.

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 available resources remained about the same.  He wrote of how populations could be limited by disease, famine, and conflict, but there was a warning embedded about growing human populations as well.  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.

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 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 merchant 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 off he 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 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 (600 miles) from the equatorial jungles of South America.  The limited types of animals there had obvious relatives on the mainland, but were different, particularly suited to the different circumstances available on the islands.  Assuming that their ancestors were groups of mainland animals who had been unlucky enough to wind up there, how did the immigrant group 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 the Fittest."  Simply put, in any given group of organisms, there will be some variety of features that directly affect how good a chance each individual has of living to reproductive age and then successfully reproducing - as a general trend, each generation of offspring will, more and more, reflect features that are advantageous to their particular environment.  The important detail here is that environments change over time - 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 which individuals reproduce (the "Selection" part) 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,  has changed 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 natural conditions they were born into.

Evolution is not an "ever upward movement toward perfection," as Lamarck and many of his time believed, although that is what it often is portrayed as even today;  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 comes with a long list of extinction threats from our own meddling, including but not limited to weapons of mass destruction), and not everything evolves at the same rate, partly because the rate at which environments change varies considerably from place to place (and even pieces within environments vary), and 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).

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 scientists.  Perhaps 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 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 1850s, 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 concept would then probably be linked only to Wallace, even though Darwin's colleagues knew he had developed the same idea;  to preserve Darwin's place in science, when Wallace's paper was made public, it was accompanied by a similar one by Darwin. 

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 was well-known in certain circles, 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, such as a peacock's tail, that had obvious advantages in the competition for mates but which might actually be disadvantages from a survival standpoint.  This was not difficult to integrate into his ideas, since it is actually mating 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 mate and what helps you actually accomplish the mating.

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 tinkerings that have adjusted it here and there.  As we continue through the history of biology, we will investigate the impact of later developments.

As said before, fossils are usually found in layers of sedimentary rocks, usually from newer surface rocks to older deep layers.  The organisms died in or near bodies of water, where they were swept off and sank to the bottom, where usually their soft parts were consumed by other organisms and only shells, bones, and teeth remained.  For large organisms, even those that lived in water would be rare in the sediments (think how separated whale carcasses must be on today's ocean floor), so it's amazing that we have much record of land animals (like dinosaurs) at all!

These ancient layers of sediment were laid down in bodies of water, and most studied 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 location was high and dry.  

Fossils can also be made when organisms are covered by sand, or tar (a rare happening), or pine sap (amber fossils), or volcanic ash (lava tends to be too destructive and produce too hard a rock) - fossil footprints often are sand that was covered by ash that dried and protected them.  Buried layers compress, lose water and accumulate minerals from the sediments around them, eventually becoming petrified, or rock-like - becoming fossils.

So what's in the fossil record?  Mostly it's 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 few fossils exist.  We may have a single individual for an entire era, and no way to know how typical it was.  Those who criticize the concept of evolution often use the gaps in the fossil record for their evidence, and it's easy to see why.

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.  

One type of comparison was championed by Ernst Haeckel in the late 1800s:  looking for similarities between the embryo forms of animals, specifically backboned animals (vertebrates).  Relating the progression in form of 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 fishy, then an amphibianlike, 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.  

But comparing embryos is very important, because evolutionary changes rarely cause major changes early, for two major reasons.  First, the earlier the change, the larger the impact, and evolution tends to work mostly in small variations rather than huge leaps.  Second, the immediate, important environment of embryos often changes little even while the environment of the adults changes.  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 a hard thing to determine.

Some of the most widespread connections have come recently, as researchers have looked into the genes responsible for very early embryo development.  These homeogenes code for proteins that determine front-and-back, right-and-left, inside-from-outside-layers, organ placement, and so on, and are turning out to be remarkably similar across wide ranges of organisms.  For example, almost the same exact gene determines eye placement in both fruit flies and mice.

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 be the same?

In some types 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.  Some species adapted quickly to such systems and have moved with them as they have migrated;  these species have also shown very little change over a very long timeframe.  Horseshoe crabs, residents of a surf ecosystem that works today probably as it has for eons, today look almost exactly like their 100-million-year-old fossil relatives.  Large free-swimming 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 (that's 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!
 

INFORMATIONAL LINKS 

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

A discussion of a lab experiment showing natural selection in action.

A basic website on evolution, with a focus on creationism's take on the origins of Life.

A transcript from an interview with a Christian biologist.