Fossils
Some friends have pointed out that in writing about the history of life on the planet, I have neglected to cover a couple of rather important topics. In today’s post, I would like to begin to redress this oversight by talking about the evidence we have that all these marvellous prehistoric creatures I’ve been writing about actually existed at all. The most important source we have are fossils, be they:
1.
fossils of the animals themselves;
Source: http://blog.stones-n-fossils.com/scavenger-hunt-fish-fossil
Source: http://www.geosociety.org/graphics/gv/PikesPeak/03FossilWasp.jpg

Source: http://www.fossilmuseum.net/Fossil_Galleries/GreenRiverFossils/Platanus_wyom ingensis/Platanus_wyomingensis.jpg
2.
fossilised trackways, coprolites (fossilised dung), and the like; or
Source: http://drscavanaugh.org/dino/images/IMG0027.jpg

Source: http://www.stanford.edu/class/humbio103/ParaSites2006/Enterobius/coprolite.jp
g
3.
other physical traces left by these animals, things like gastroliths (stomach-stones).
Source: http://skywalker.cochise.edu/wellerr/students/gastrolith/project.htm
In the case of more recent animals, we have either:
1.
sub-fossils (remains whose fossilisation is not complete, either because they are not old enough, or because the conditions under which they were buried were not optimal for fossilisation); or

Source: http://www.fossils.duke.edu/research/images/limbbones.JPG
2.
actual remains: bones, teeth, bits of skin or feathers etc. which have usually been: a.
mummified ( i.e.
died in an extremely dry and sterile environment, and been desiccated before decomposition could occur).
Source: http://windyharbor.wordpress.com/2008/01/06/sunday-scienceupdate-1/ (N.B. This is a dinosaur which died, was mummified, and then fossilized)

b.
buried in tar (as for example at the famous tar pits in La Brea);
Source: http://la-brea-tar-pits.visit-los-angeles.com/Columbian-
Mammoth.jpg
Source: http://discounthotels.com/travel-blog/wpcontent/uploads/2009/07/la-brea-tar-pits.jpg c.
encased in amber (which is in fact aged and transformed tree resin (not sap) – sometimes people refer to it as fossilised resin, but the process by which resin becomes amber (or resinite to give it its proper name) is not the same as that by which say dinosaur bones become dinosaur fossils. In fact, amber is resin which has been polymerised naturally by temperature and pressure). If you’ve watched ‘Jurassic Park’, you will recall that in the movie, they obtained the dinosaur DNA from insects trapped in amber.
This is not at all far fetched. Traces of DNA have in fact been extracted

from the stomachs of insects trapped in amber. However, we have no way at present of knowing what animal that DNA came from;
Source: http://www.don-lindsay-archive.org/creation/amber_work.jpg d.
entombed in ice (usually in glaciers); or

Source: http://i682.photobucket.com/albums/vv181/USMBCount2100/AmazingEar thScenes12.jpg
Source: http://amandainmaine.wordpress.com/2009/04/21/a-near-perfectfrozen-mammoth-resurfaces-after-40000-years/ e.
captured in the records and sketches of people who got to see these animals before they became extinct (as was the case with the dodo, say), or even, in the case of recently extinct animals (like the thylacine for example) captured in photographs and on movies!

Source: http://www.davidreilly.com/dodo/images/gallery/DODO1.jpg
Source: http://diogenesii.wordpress.com/2009/09/07/september-7-1936-a/
Most of the other remains are fairly straightforward, and do not need much more in the way of explanation, but fossils are a bit more complicated, so I am going to devote the rest of this post to fossils. The main question to ask is what are fossils, how are they formed, and how much can we learn from them?
The word comes from the Latin verb, fodere (to dig) from which the Latin noun fossus (having been dug up). Basically, fossils are formed whenever an animal is relatively quickly buried under certain conditions, such that the organic material in the buried remains are gradually replaced by water-borne minerals (keep in mind though that this is all derivative knowledge; because the process of fossilisation takes so long no one has done a fossilisation-experiment – it would take millions of years to run such an experiment, and who’s got that much time? Besides, we ourselves would have evolved before the experiment were completed!).
In every day use in fact, the word is a bit misleading, as it often serves as a blanket noun for a variety of processes, all of which end up producing a cast of sorts from a living thing.
The earliest fossils we have date from about 3,850,000,000 years ago, which is
(geologically speaking) not that much after the earth itself formed, and the ‘newest’ fossils are a mere 10,000 years old – this is an arbitrary cut-off date, and the remains of living things that are 10,000 years old are chemically utterly different from the remains of things that are hundred or thousands of millions of years old.
If you were to look at some fossils, the first thing that would strike you is that they look like stones, as friends of mine, looking at my fossil collection have often remarked.
Well, that is because they are stone: they are animal parts which have been mineralised.
The animal’s hard parts (bones, shells, teeth etc.), and occasionally other, softer parts
(hair, skin, etc.) have become stone.

How does this process work? I have copied this from http://www.discoveringfossils.co.uk/whatisafossil.htm
but have modified the text somewhat. The most common way for a fossil to form is when the dead life-form is rapidly covered immediately after death by fine-grained material – the finer the better, as this affects how much detail is preserved. The covering material could be sand, silt, clay, ash, etc, but it needs to be inorganic matter for fossilisation to occur.
In the following example a fish is used to illustrate the stages associated with fossilisation within off-shore marine sediments. This is just one summarised, and surmised example, in reality there are countless scenarios that create the conditions necessary for fossilisation in marine sediments.
Death
Having reached adulthood and returned to its birth place to spawn, this particular fish reaches the end of its life and dies. Soon after death the body of the fish becomes water-logged and sinks to the seafloor (note that quite often the gases produced during decomposition cause the carcass to float back to the surface, so the final resting place may be some distance away). More often than not the carcass would be pulled apart and scattered by scavenging crustaceans and other fish, however on this occasion the absence of any large scavengers leaves the fish relatively undisturbed.
Left: A fish returns to its birth place to spawn. Right:
Having spawned the fish dies and shortly after sinks to the seafloor.

Although fossils can be found in sediments deposited in turbulent (high energy) environments near the coastline, complete/articulated skeletons require undisturbed conditions. A quiet seafloor with minimal light, low oxygen levels and a soft muddy composition are among the preconditions suitable for preserving organic remains.
Decay and burial
After several weeks the fish is partially decomposed.
Despite the calm conditions on the seafloor, several thousand meters into the bedrock pressure is building along an active geological fault. Suddenly the stressed rock slips, sending shockwaves to the rock above and causing the sediment nearby to mobilise. The mobile sediment travels across the seafloor burying the fish in the process, in what is often termed a rapid burial event.
Rapid burial events are good for fossilisation of complete specimens. Once entombed beneath the sediment the remaining flesh and soft tissue are broken down by bacteria, leaving just the skeleton in the position of burial.
Left: After several weeks the soft body tissues have mostly decayed. Right: Tectonic activity induces nearby sediment to mobilise, burying the fish in the event.
Rapid burial is a common component for optimal fossilisation, as prolonged exposure would otherwise increase the likelihood of disturbance from scavengers and/or currents. Burial may also occur quickly if a high volume of sediment is deposited in the area following a period of heavy rain that delivers sediment from major rivers (for example).

Sediment accumulation and permineralisation
Over time the skeleton is gradually buried deeper by accumulating sediment. Slowly the weight of the sediment compacts the underlying areas, pressing the grains together, driving excess water out, and depositing minerals in the pores, and ultimately turning the soft sediment to hard rock - a process known as lithification.
As this process takes place, minerals contained within the water-saturated sediment replace the original minerals in the skeleton and fill any voids formed as parts of the skeleton dissolve. The process of mineral replacement is known as permineralisation and results in a re-mineralised copy of the original skeleton.
Left: Several months pass and all that remains of the buried fish is its skeleton. Right: As times passes more sediment accumulates above the fish and the skeleton is gradually compressed and permineralised.
Uplift and exposure
Many millions of years pass and the rock remains buried deep within the bedrock; however tectonic forces associated with the collision between neighbouring continental plates have begun to buckle and uplift the bedrock, raising it above sea level and exposing it to erosion. Gradually, the exposed rock is stripped away, until eventually the top of the fish's skull is visible at the surface.

Left: Over time the rock is distorted and uplifted by geological forces associated with continental movement, raising it above sea level.
Right: The uplifted rock is exposed to weathering and gradually erodes away, eventually exposing the tip of the fish's skull at the surface.
Discovery and extraction
Finally, having lain beneath the ground for millions of years, the partially exposed skull is spotted by a palaeontologist, who undertakes a careful extraction of the skeleton. The process requires patience and precision work to avoid damaging the specimen; a generous amount of rock is retained around the specimen to protect it.
Left: A palaeontologist recognises the fish by the small area of skull exposed and begins to carefully extract the specimen. Right: A Pomognathus fish from Houghton Quarry
- the skull is clearly visible, and what parts of the skeleton remain are obscured within the chalk matrix.
On a light note, many dinosaur fossils have been found in England. The earliest known dinosaur fossil in England was discovered in 1676 by Reverend Plot, who found a

femur. On discovering his archaeological find, Reverend Plot concluded that it was that of a giant!
So, now that you know what fossils are and how they are formed, let’s move on to the question of how can we use them to discover things about the animals from whom they came. At the most basic level, we can put the fossils remains together, and get a sense of how the animal’s skeleton looked. In doing this, we follow certain empirical rules.
For example, have you ever noticed that you and your chicken dinner both have very similar skeletons? You both have a back-bone, and a breast-bone, from both of which ribs sprout; you both have 4 limbs, which have a particular structure, first a single bone (upper arm / thigh), then a double bone (lower arm / shin), and finally a bunch of little bones (fingers / toes). You both have a neck, composed of a bunch of vertebra, and a skull which is composed of a bunch of bones fused together, and one set of bones which is loosely attached (the lower jaw). You both even have the vestiges of a tail! Internally, the story repeats itself: 1 heart; 1 liver; 2 kidneys; 1 set of lungs; 1 brain, located at one end of your spinal column; etc. True, you don’t have a gizzard, and you don’t have feathers, but you’re getting the picture I hope.
This pattern is repeated in all quadrupeds, with certain variations ( e.g
. the number of bones in the spines or necks of various animals is not always the same, and certain animals have structures that others do not have, but these are minor details. The important thing is that there really are these consistent uniformities. Thus, if you were to find the partially complete skeleton of a new quadrupedal animal, you would look for the same patterns: say you only found one rear leg, and half a hip, you would expect there to be only one other rear leg (which would follow the 1-bone, 2-bone, many-bone basic plan) and the other half of a bowl-shaped hip. You would not expect 2 or 3 more legs, or some other ordering of limb bones.

Source: http://www.krassesrudel.at/forumbilder/thecoop/figure3.gif

Source: http://www.horseracinghistory.co.uk/hrho/jsp/education/skeleton.jsp
If you look at these three skeletons above, you will see just what I’m talking about: They all share the same basic skeletal-, muscle-, and organ-plan.
The fact that there is this basic quadrupedal body-plan in nature incidentally is excellent evidence for evolution: the basic body-plan exists precisely because all quadrupeds evolved, ultimately, from some common ancestor which was built that way.
The skeleton which you put together would allow you to take matters much further than that though: we know that all animals today use muscles to move themselves, and that these muscles are attached to the bones at particular points, and in particular ways. We also know that where muscles attach to bone, they leave a particular trace, and that this trace is large for large muscles, and small for small ones. Using this empirical fact, you can get an estimate of the sizes the various muscles would have been on the animal you are investigating, and based on that you could work out how the animal might have looked (though not what colour it was).
You could take this much further though. Based on biomechanical studies, you could also work out things like how fast it could have run, how strong its bite would have been, how strong its bones etc. This in turn would have allowed you to speculate meaningfully on whether the animal was say a chase and attack hunter, an ambush hunter, or a scavenger (scavengers need very strong teeth and jaws usually, because they often
(though not always) crack bones to get at the marrow inside. Swift running hunters usually cannot crack bones because the equipment necessary to do this would be too heavy, and thus would interfere with their swift running abilities: This is why cheetahs and hyenas have such very different skeletal structures.

Based on other factors, like how the fossils you’ve found are disposed, you could work out many other behavioural things about your fossil animal: for example, if you often found the fossils of several members of the same species together, you could reasonably conclude that it was a social species; if you found the bite-marks of species A on the bones of species B, you could conclude that A preyed on B; if you found that bitemarks from severe, incapacitating bites showed signs of healing, you could conclude that maybe this was a social species in which other members took care of, or at least fed injured members of the pack; if you found a fossilised nest, and egg-shells which showed signs of trampling, you could conclude that the mother, father, or both of this particular species nursed their young after hatching (trampling implies that the young hung around the nest for some time after birth, and this implies some parental care); on the other hand, if you found the opposite, un-trampled eggshells, then you might reasonably conclude that in this species the young were mobile soon after birth, and either did not need parental care, or were able to run soon after birth, and took off running with their parents.
Thus, by combining the fossils themselves with a bit of serious thinking about what further knowledge can be extracted from them, we can draw quite a lot of conclusions from the fossil record, and even take reasonable stabs at working out unfossilisable things like behaviour. The scientific method and logic are truly wonderful things.