A simple Geology principle known as superpositioning describes how lower strata tend to be older than the strata above them. The existence superpositioned layers is caused by the deposition that takes place over the different Geological eras. Erosion takes away from these sediment layers. So while the order of successive layers are consistent, the layers for each Geological era do not exist in uniform sediment thickness, because desposition and erosion do not happen uniformly throughout the world, nor at the same time.
Simple physics (ie. gravity) and common sense makes it apparent that the lower strata are older as they have to be formed in order for more sediment to be deposited above them. There are a few exceptions to this of course; thrust faults and folds for examples can cause contortions in the layers. The existence of folds and thrust folds have are well understood and can be checked for, and they are by and far the exception to the rule.
The Geophysics principles mentioned above were actually known before Darwin's voyage on the Beagle, and were therefore not created for the sake of arguing evolution. Rather Evolution is in fact, largely born of the Geological history and the order of the fauna within. The men who founded modern Geology were in fact Christian, which is why Old Earth Creationism (known today as Progressive Creationism, and is sometimes mixed and matched with Theistic Evolution) predates the theory of Evolution. The geologic column and the law of faunal succession show us that the Earth's fauna have appeared in a certain order, and Evolution simply explains the cause of this reality.
To oversimplify what we find in these successive layers; we find fish before we find amphibians, which we find before we find reptiles, which we find before we find birds. A similar succession of fauna can be applied to the faunal succession leading to humans and whales. Furthermore, we find representations of transitional fossils ("in betweens") in the layers we'd expect them to if certain orders of animals evolved from others.
So for example, we find Archaeopteryx (a bird with reptilian features not found in modern day birds) in the layers of the Jurassic while we don't find modern birds until the upper layers. Conversely, we don't find birds in the strata below Archaeopteryx. It's clear that birds evolved from reptiles. Whether they did so from therapod dinosaurs (as most Paleontologists claim) or from non-dinosaur archosaurs (still a reptile) as a smaller minority claim, the point is still the same; reptiles with bird-like features and birds with reptilian features both appear during the Jurassic period (before modern birds but well after the first reptiles).
Whales are another example of faunal succession. We don't find whales in the same strata as any of the ancient Devonian fish. Rather, we only find them in the strata well above Devonian period. This would not be the case if they "appeared" at the same time as the first fish. Furthermore, there exist a few examples of fossilized transitions between land mammals and whales. Between fossilized mammals such as Pakicetus, Ambulecetus Natans, and Basiliosaurus, who show up in the fossil record well after the first mammals appear but well before modern whales do, it's clear that whales evolved from land mammals with physical characteristics similar to sea lions. The transition in pelvis, blow hole, and legs to flippers are accounted for in this sequence of animals with semi-aquatic features.
Given the succession of fossils we find in the strata, its clear that the first animals were sea dwelling creatures. Land dwelling creatures show up later (higher) in the strata. In between these two we find fossils that are clearly transitional between fish and amphibians. The succession of these creatures all follow the same basic body pattern, which tells us that the Earth's fauna share common ancestry. Furthermore, the fauna found in the upper layers become more and more diverse. At some point the only tetrapods we find are fish-amphibians. But as we move 'higher' in the strata, we find more and more diversity as we begin to find different types of reptiles in greater numbers and diversity, and eventually mammals and birds as well, also in greater numbers and diversity within each off these groups as we move higher in the strata. Furthermore, the fauna we find in the upper layers closer resemble their contemporary counterparts than what we find in the layers below.
These Paleontological discoveries can and are also cross-referenced by Geographic location of fossils, in addition to the homological and vestigial structures in modern day fauna (since the Geological record showcases faunal succession that leads to what we have now).
Both ape and early-to-mid hominid fossils are only found in Africa and Asia which, consequently happens to be the only place where modern day apes exist. Again, there is no reason why this should be the case, unless they evolved more recently than say, monkeys, which do inhabit other parts of the world. Again, primates such as monkeys show up well before later primates.
Speaking of apes and hominids; Paleoanthropology reveals a group of hominids that demonstrate the intermediate steps between ape and humans. From Australopithecus Afarensis and Africanus, Homo Rudolfensis, Habilis, Ergaster, Antecessor, and Archaic Homo Sapien to modern Homo Sapien, we see a gradual increase in brain size; from 410 CC (about the size of a Chimpanzee) to modern homo sapiens (1300 CC). Not only this, but we find that the gradual increase in brain size is accompanied by other features that become less and less ape-like, and more and more human. Brow Ridges, Sagittal Crests, Jaw sizes, and the spine becomes better adapted for bipedalism. Hominid fossils provide such a clear gradient that Creation scientists can't seem to agree which are ape and which are human.
Faunal succession shows us that tails have been common in all tetrapods that lead to apes, who, like us, contain a vestigial tail (coccyx). The fossil record also shows that our ancestors, much like today's great apes, had large powerful molars for which to chew thick vegetation. In humans, this results in wisdom teeth; vestigial teeth whose poor structure cause pain in one third of adults and in some cases, can even cause death. Coincidentally, hominid fossils show a succession towards smaller and smaller jaws which would indeed result in this crammed nature of the human jaw.
In regards to snakes, fossils like Pachyrhachis problematicus make it clear that snakes evolved from legged reptiles. Not only do we find fossilized snakes with small but pronounced legs, we find them in the East, where modern day Pythons exist. Coincidentally some Pythons have leg remnants.
Creationists have indeed raised objections to the fossil record. But they are based on a general misunderstanding of the Geologic Column. A few examples;
The Geologic Column doesn't exist/is mostly missing/only exists in text books, etc.
This stems from a common misunderstanding of what the geologic column is. Some creationists think of it a place, like Mount Rushmore and sarcastically ask "where is it then?" Others believe that a certain level of sediment must exist for the layers for the column to be real and tend to come up with interesting numbers in regards to the miles of sediment that "should" exist for the column to be real. What they appear to do is take the maximum height of sediment found for specific eras in different parts of the world, and create hypothetical "height requirement" for superpositioned layers and sometimes argue that should all exist in the same parts of the world.
This however, is a gross misunderstanding of Geophysics as there is no reason to believe that sedimentation (which creates the layers) nor erosion (which chips away from them), should happen uniformly among different parts of the world.
What makes the column and faunal succession a reality is the fact that we find the same sets of fauna in the same layers throughout the world. The Geologic Column therefore represents a series of sedimentary layers that can be cross-referenced and validated or falsified. 200 years of Geology has only served to solidify the reality of faunal succession.
There are certain theoretical findings that would indeed falsify faunal succession; like finding spear points in a Triceratops (as we do in mammoths). A fossil (or even a living animal) that fell outside of the same pattern of animal would also provide falsification. Whether contemporary or solely in the fossil record, a 6-legged mammal, a bird with wings plus 4 appendages, or a spider with wings would not be explainable within the confines of the evolutionary tree, yet "explicable" by "separate creation." Instead, we find fauna that not only existence in sequence, but do so in a limited pattern. Adaptation explains why the world's fauna would appear in this manner, whereas a conscious creator would have no pattern or timeline to have to adhere to.
Polystrate trees and fossils.
Creationists often assert that fossils or objects such as trees that penetrate a certain amount of sediment and therefore existing in a "polystrate" manner, disprove the Geological consensus that these layers represent different Geological eras. However, the problem with this argument is that it ignores 2 basic geological principles; rapid sedimentation, and cross-cutting.
Rapid sedimentation can be caused by a number of geological occurrences, including floods and landslides. Often times this provides for the best preservation of fossils as it causes for a quick burial that allows the creature to be preserved intact as it avoids being torn to pieces by predators or scavengers, and the carcass is shielded from erosion (assuming is doesn't become unearthed by other occurrences, thereby being exposed to such). Such rapid sedimentation also has the ability to bury trees in such quick fashion and hence, we find "polystrate trees" from time to time.
Then there is the simple principal of Cross-Cutting; an object which cuts through sediment must be younger than the sediment its cuts through (this is common sense as an object can't cut through sediment that doesn't exist yet). It's a known Geological fact that layers of strata can be penetrated by newer objects. One example of this would be a water logged tree being dragged down into mud, which can take centuries to harden. Creationists often use these instances as 'proof' that the Earth's sediment must be young.
Folds and thrust faults can also cause the layers to overlap and overturn. Again, these are Geological occurrences that have been known and checked for. They are nothing new, but Creationists tend to ignore them and instead look for discrepancies wherever they think they can find them.
The Geological record clearly shows a succession of species that appear from simple to complex, form sparse in diversity to more abundant. It is clear that over time, different creatures 'appeared' to fill more and more specific niches, and the pattern displayed in the record, seamlessly leads up to modern day fauna. Evolution explains this fact.
