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A method for scientists to compare animals from the past to present day animals is through comparing fossil records to try and link common ancestors

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Fossil Evidence

The fossil record provides snapshots of the past that, when assembled, illustrate a panorama of evolutionary change over the past four billion years. The picture may be smudged in places and may have bits missing, but fossil evidence clearly shows that life is old and has changed over time.

Early fossil discoveries

In the 17th century, Nicholas Steno shook the world of science, noting the similarity between shark teeth and the rocks commonly known as "tongue stones". This was our first understanding that fossils were a record of past life.

Two centuries later, Mary Ann Mantell picked up a tooth, which her husband Gideon thought to be of a large iguana, but it turned out to be the tooth of a dinosaur, Iguanodon. This discovery sent the powerful message that many fossils represented forms of life that are no longer with us today.

Gideon Algernon Mantell was an English obstetrician, geologist and palaeontologist. His attempts to reconstruct the structure and life of Iguanodon began the scientific study of dinosaurs: in 1822 he was responsible for the discovery (and the eventual identification) of the first fossil teeth, and later much of the skeleton, of Iguanodon. Mantell's work on the Cretaceous of southern England was also important.

Nicholas Steno's anatomical drawing of an extant shark (left) and a fossil shark tooth (right). Steno made the leap and declared that the fossil teeth indeed came from the mouths of once-living sharks.

Nicolas Steno was a Danish pioneer in both anatomy and geology. Already in 1659 he decided not to accept anything simply written in a book, instead resolving to do research himself. He is considered the father of geology and stratigraphy.

The first fossil found in the United States was that of a thigh bone found by Dr. Caspar Wistar in Gloucester County, New Jersey, in 1787, but has been lost since its discovery. Other fossils have been documented in this area.

The first nearly-complete dinosaur skeleton was found by William Parker Foulke in Haddonfield, New Jersey on an excavation that began in 1838, and continued through 1858.

Additional clues from fossils

Today we may take fossils for granted, but we continue to learn from them. Each new fossil contains additional clues that increase our understanding of life’s history and help us to answer questions about their evolutionary story. Examples include:

Indication of interactions

This ammonite fossil (see below) shows punctures that some scientists have interpreted as the bite mark of a mosasaur, a type of predatory marine reptile that lived at the same time as the ammonite. Damage to the ammonite has been correlated to the shapes and capabilities of mosasaur teeth and jaws. Others have argued that the holes were created by limpets that attached to the ammonite. Researchers examine ammonite fossils, as well as mosasaur fossils and the behaviors of limpets, in order to explore these hypotheses.

Clues at the cellular level

Fossils can tell us about growth patterns in ancient animals. This is a cross-section through a sub-adult thigh bone of the duckbill dinosaur Maiasaura(below). The white spaces show that there were lots of blood vessels running through the bone, which indicates that it was a fast-growing bone. The black wavy horizontal line in mid-picture is a growth line, reflecting a seasonal pause in the animal’s growth.

Examples of Evolution

The fossil record contains many well-documented examples of the transition from one species into another, as well as the origin of new physical features. Evidence from the fossil record is unique, because it provides a time perspective for understanding the evolution of life on Earth. This perspective is not available from other branches of science or in the other databases that support the study of evolution.

Evolution of vertebrate legs

The possession of legs defines a group of vertebrate animals called tetrapods - as distinct from vertebrate animals whose appendages are fins, the fishes. In most fishes, the thin bony supports of the fins are arranged like the rays of a fan; hence these fishes are called 'ray-finned' fish. Trout, perch, and bass are examples of living ray-fins.

Certain fishes are called 'lobe-finned,' because of the stout, bony supports in their appendages. Lobe-finned fish first appear in the fossil record in early Late Devonian time, about 377 mya. The bony supports of some lobe-finned fishes are organized much like the bones in the forelimbs and hind limbs of tetrapods: a single upper bone, two lower bones, and many little bones that are the precursors of wrist and ankle bones, hand and foot bones, and bones of the fingers and toes that are first known in Late Devonian amphibian-like animals from about 364 mya. These animals were the first tetrapods. Many similarities also exist in the skull bones and other parts of the skeleton between Devonian lobe-finned fishes and amphibian-like tetrapods. In fact, in certain fossils the resemblances are so close that the definition of which are fish and which are tetrapods is hotly debated.

In 1998, a lobe-finned fish was described from Upper Devonian rocks from about 370 mya in central Pennsylvania (Daeschler and Shubin, 1998). This fish has bones in its forelimb arranged in a pattern nearly identical to that of some Late Devonian amphibian-like tetrapods. The pattern includes a single upper-arm bone (humerus), two forearm bones (radius and ulna), and many little bones connected by joints to the forearm bones in the positions of wrist and finger bones. However, the finger-like bones look like unjointed fin rays, rather than the truly jointed finger bones of tetrapods. Should the animal be called a fish or a tetrapod? It's hard to say. On the basis of the finger bones, it could be classified as a fish, whereas, on the basis of the large limb bones, the animal could be classified as a tetrapod.

Remember that we humans created the classification scheme for life on Earth, and we choose where to draw the boundaries. When dealing with transitional forms of life this is not an easy task!  You make a very valid point.  Classification  is arbitrary and may change with additional information. Just look at how DNA  is effecting the evolutionary tree. So much so we've dropped the "tree" and go with clades

Fossils such as this one help scientists determine ancestry and common relationships with modern species. Comparing a fossil like this to a modern day lizard is reasonable considering the similar body structure and organs

Evolution is a fact in the sense that life has changed through time. In nature today, the characteristics of species are changing, and new species are arising. The fossil record is the primary factual evidence for evolution in times past, and evolution is well documented by further evidence from other scientific disciplines, including comparative anatomy, biogeography, genetics, molecular biology, and studies of viral and bacterial diseases. Evolution is also a theory – an explanation for the observed changes in life through Earth's history. Evolution is an elegant theory that explains the history of life through geologic time; the diversity of living organisms, including their genetic, molecular, and physical similarities and differences; and the geographic distribution of organisms. Evolutionary principles are the foundation of all basic and applied biology and paleontology, from biodiversity studies to studies on the control of emerging diseases. Because evolution is fundamental to understanding both living and extinct organism. The unifying theory of evolution will become an even more powerful explanation for the history of life on Earth.

Here is a good clip the in a way debate whether paleontology was and is the main cause for evolution. Fossils are a record of change not a cause!

Youtube clip removed. Basically claptrap. Right off the bat the guy starts talking about the origen of life. Evolutuion is the origen of sp.  Then he chooses to omit most of the fossil evidence and points only to what supports his claim.  Fossil evidence is only one of several that form a coherent whole.

Further evidence supporting paleontology is such that when organisms die, they often decompose rapidly or are consumed by scavengers, leaving no permanent evidences of their existence. However, occasionally, some organisms are preserved. The remains or traces of organisms from a past geologic age embedded in rocks by natural processes are called fossils. They are extremely important for understanding the evolutionary history of life on Earth, as they provide direct evidence of evolution and detailed information on the ancestry of organisms. Paleontology is the study of past life based on fossil records and their relations to different geologic time periods.

For fossilization to take place, the traces and remains of organisms must be quickly buried so that weathering and decomposition do not occur. Skeletal structures or other hard parts of the organisms are the most commonly occurring form of fossilized remains. There are also some trace "fossils" showing moulds, cast or imprints of some previous organisms.

As an animal dies, the organic materials gradually decay, such that the bones become porous. If the animal is subsequently buried in mud, mineral salts will infiltrate into the bones and gradually fill up the pores. The bones will harden into stones and be preserved as fossils. This process is known as petrification. If dead animals are covered by wind-blown sand, and if the sand is subsequently turned into mud by heavy rain or floods, the same process of mineral infiltration may occur. Apart from petrification, the dead bodies of organisms may be well preserved in ice, in hardened resin of coniferous trees, in tar, or in anaerobic, acidic peat. Fossilization can sometimes be a trace, an impression of a form. Examples include leaves and footprints, the fossils of which are made in layers that then harden.

Rock forms in layers called sediment. In the deepest layer of sediment there are fossils, and the newest layer is the ground we stand on today. Below is an example of sedimentary layers.

Methods

A method that paleontologists can use is Radiometric Dating- This relies on half-life decay of radioactive elements to allow scientists to date rocks and materials directly. The picture below is an example of radiometric dating:

Also once the paleontologists have dug up the fossils and bones they'll compare them to others to see if they're either:

Analogous Structures- Structures in different species that look alike or preform similar functions developed convergently but have not developed from a similar group/structure.

 Ex: spikes of hedgehog and porcupine

OR

Homologous structures- Same structure but different function

Techniques and Principles of Paleontology

Taken together, fossils can be used to construct a fossil record, which is a timeline of fossils reaching back through history. Several factors must be taken into account when constructing such a record. The strata of rock in which fossils are found give us clues about their relative ages. Similarly, new technological techniques such as radioactive carbon dating help determine the absolute ages of fossils. In addetion to supplying a fossil's relative age, rock strata can also give clues about the environments in which an animal or plant lived. The chemical make-up of these strata can tell us the balance of gases in ancient atmospheres. Major cataclysmic events such as eruptions and meteor strikes also leave there mark on the fossil record.

There are, however, limitations on the information fossils can supply. Fossilization is an improbable event. Most often, bones and other materials are crushed or consumed before they can be fossilized. In addition, fossils can only form in areas where sedimentary rock is formed, such as ocean floors. Organisms that live in these environments are therefore more likely to be fossilized. Erosion of exposed rock faces or through the crushing action of geological movements can destroy fossils even after they are formed. All of these conditions lead to large and numerous gaps in the fossil record.

Evolution of vertebrate legs

The possession of legs defines a group of vertebrate animals called tetrapods - as distinct from vertebrate animals whose appendages are fins, the fishes. In most fishes, the thin bony supports of the fins are arranged like the rays of a fan; hence these fishes are called 'ray-finned' fish. Trout, perch, and bass are examples of living ray-fins.

Certain fishes are called 'lobe-finned,' because of the stout, bony supports in their appendages. Lobe-finned fish first appear in the fossil record in early Late Devonian time, about 377 mya. The bony supports of some lobe-finned fishes are organized much like the bones in the forelimbs and hind limbs of tetrapods: a single upper bone, two lower bones, and many little bones that are the precursors of wrist and ankle bones, hand and foot bones, and bones of the fingers and toes that are first known in Late Devonian amphibian-like animals from about 364 mya. These animals were the first tetrapods. Many similarities also exist in the skull bones and other parts of the skeleton between Devonian lobe-finned fishes and amphibian-like tetrapods. In fact, in certain fossils the resemblances are so close that the definition of which are fish and which are tetrapods is hotly debated.

In 1998, a lobe-finned fish was described from Upper Devonian rocks from about 370 mya in central Pennsylvania (Daeschler and Shubin, 1998). This fish has bones in its forelimb arranged in a pattern nearly identical to that of some Late Devonian amphibian-like tetrapods. The pattern includes a single upper-arm bone (humerus), two forearm bones (radius and ulna), and many little bones connected by joints to the forearm bones in the positions of wrist and finger bones. However, the finger-like bones look like unjointed fin rays, rather than the truly jointed finger bones of tetrapods. Should the animal be called a fish or a tetrapod? It's hard to say. On the basis of the finger bones, it could be classified as a fish, whereas, on the basis of the large limb bones, the animal could be classified as a tetrapod.

Remember that we humans created the classification scheme for life on Earth, and we choose where to draw the boundaries. When dealing with transitional forms of life this is not an easy task!

http://www.ucmp.berkeley.edu/paleo/paleowhat.html This link is very helpful in explaining different types of paleontology, as well as the field of paleontology in general.

This video is very helpful and discusses that fossils show a change over time in animals, which supports the idea of evolution.  It talks about how animals "modify" themselves.  It shows paleontologists digging up fossils in order to see if the "historical timeline" points to evolution.  It also supports "VISTA".  

Paleontology is the study of prehistoric life including organisms' evolution and interactions with each other and their environments. As a "historical science" it tries to explain causes rather than conduct experiments to observe effects. Paleontological observations have been documented as far back as the 5th century BC. The science became established in the 18th century as a result of George Curvier's work on comparative anatomy and developed rapidly in the 19th century. Fossils found in China since the 1990s have provided new information about the earliest evolution of animals, early fish, dinosaurs and the evolution of birds and mammals. Paleontology lies on the border between biology and geology, and shares with archeology a border that is difficult to define. It now uses techniques drawn from a wide range of sciences. As knowledge has increased, paleontology has developed specialized subdivisions, some of which focus on different types of fossil organisms while others study ecological and environmental history, such as ancient climates.

Limitations

The fossil record is an important source for scientists when tracing the evolutionary history of organisms. However, because of limitations inherent in the record, there are not fine scales of intermediate forms between related groups of species. This lack of continuous fossils in the record is a major limitation in tracing the descent of biological groups. Furthermore, there are also much larger gaps between major evolutionary lineages. When transitional fossils are found that show intermediate forms in what had previously been a gap in knowledge, they are often popularly referred to as "missing links".

There is a gap of about 100 million years between the beginning of the Cambrian period and the end of the Ordovician period. The early Cambrian period was the period from which numerous fossils of sponges, jellyfish, snails and arthopods are found. The first animal that possessed the typical features of vertebrates, the Arandaspis, was dated to have existed in the later Ordovician period. Thus few, if any, fossils of an intermediate type between invertebrates and vertebrates have been found.

Some of the reasons for the incompleteness of fossil records are:

• In general, the probability that an organism becomes fossilized is very low;
• Some species or groups are less likely to become fossils because they are soft-bodied;
• Some species or groups are less likely to become fossils because they live (and die) in conditions that are not favourable for fossilization;
• Many fossils have been destroyed through erosion and tectonic movements;
• Most fossil are fragmentary;
• Some evolutionary change occurs in populations at the limits of a species' ecological range, and as these populations are likely to be small, the probability of fossilization is lower.
• Similarly, when environmental conditions change, the population of a species is likely to be greatly reduced, such that any evolutionary change induced by these new conditions is less likely to be fossilized;
• Most fossils convey information about external form, but little about how the organism functioned;
• Using present-day biodiversity as a guide, this suggests that the fossils unearthed represent only a small fraction of the large number of species of organisms that lived in the past.

Although this video is very long, it's really helpful to watch the full thing and a professors view on evolution and the evidence based on paleontology

Evidence of Hominids in Fossils:  A fossil is an estimated 3.3 million year old skull fossil of a Australopithecus Afarensis child.  The rest of the fossil includes a hyoid bone, limb and rib fragments, and collar and shoulder bones.  There are features in the fossil to prove that it walked on two legs like a human, although many of its features, like its finger bones shaped like that of a chimpanzee.  This fossil was the same species as Lucy, and its characteristics of both homo sapians and primates supports the theory of evolution.   

This is the piece of fossil that is from an Australopithecus Afarensis child.  It supports the theory of evolution through paleontology and it was found in Ethiopia.

This video explains how fossils are made, which can be an important fact in how paleontologists figure out what animal the fossil was.  By looking at different fossils, they can see if they are similar, in order to support evolution.

This video shows how evolution is present in fossils.  It shows how paleontologists date rocks from past to present, and how they can see the modifications to the animal in the fossils  clearly, judging from the age of the fossils (from their position in the rock).         http://www.hhmi.org/biointeractive/media/stickleback_fossil_record-lg.mov

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