Re: What are chemical details of fossil formation.

Peter:

You have asked quite a few questions, some of which have highly technical 
answers. I will do my best to get you started with some answers, but 
geochemistry is a complex and rapidly advancing field. Some of your 
questions can only be adequately answered by reference to the current 
scientific literature on geochemistry. You probably can get some help from 
a paleontologist or geochemist at the nearest university or geological 
survey.

Your first question is: what happens when organic materials like wood or 
bone are replaced, and secondarily, do partially transformed fossils exist. 
The answer to the second part is yes, partially transformed fossils do 
exist. However, many fossilization processes occur pretty fast compared to 
the age of fossils. We can look at fossilization processes operating today, 
and see the effects in very young fossils (thousands of years old). 
For example, organic material in hot springs can become 
completely encased in calcium carbonate crystals in only hours. Therefore, 
any fossil that is millions of years old has had time, at least, to become 
fully mineralized. 

The answer to the question of how mineralization takes place is more 
complicated, because there are many ways. The most common method of 
preservation for both wood and bone is probably mineralization in which 
minerals are deposited within the open spaces of the wood or bone. Wood and 
bone are very porous (at least when they have dried and the protoplasmic 
components are gone) -- this means a large amount of the inside of a piece 
of wood, say, is open space where cells used to be. Minerals are 
precipitated from water in these spaces, filling them up. This makes the 
wood heavy, hard, and changes its color, but it preserves the detailed 
structure down to the level where cells appear as units. The soft cells 
themselves are not preserved, only the spaces where they once existed. 
Therefore, the internal components of cells are not preserved by this 
method. Why do the different parts of fossil wood and fossil bone look 
different? The two main reasons are different minerals and different holes. 
Where holes are of different sizes and different spacing, the resulting 
mineral patterns will look different macroscopically. Also, over time, more 
than one mineral may be formed within a fossilizing piece of bone or wood, 
and different minerals have different colors.

Sometimes, mineralization works differently. For instance, the oldest 
fossils in the world are microorganisms preserved in chert. Chert is silica 
(SiO2), and has the same chemical composition as quartz. However, the 
crystals of chert are very very tiny, far too small to see with a 
low-powered microscope. Chert can form as a gel (like jello) within 
sediment, growing crystal by crystal, and often completely enveloping tiny 
objects that were in the sediment. The microfossils in chert can preserve 
the shapes and sizes of individual cells, but they do not usually preserve 
any information about what was inside the cells. This is because the 
toughest part of a microorganism's cell is the outside (not just a 
membrane, but an extra protective organic coating), and this is the only 
part that can usually survive being entombed in silica. 

Of course, sometimes organic material IS preserved in fossils. We know this 
because that is what coal is, that is what most plant fossils are, and 
there is organic material in some animal fossils too, such as some insects 
preserved in amber. However, most organic molecules are fragile (physically 
and chemically). The elements composing organic material (chiefly carbon, 
hydrogen, oxygen, and nitrogen) are not fragile. But the pressure and heat 
and chemical environments that affect buried organic matter usually change 
it drastically. This is where oil comes from. The oil is organic, it used 
to be parts of living creatures, and we can even tell by looking at the 
kinds of organic molecules in a particular sample of oil whether higher 
plants, algae, or other kinds of organisms sourced that particular oil. 
However, most people do not consider oil to be fossils. When we speak of 
fossilized organic matter, we mean protein such as collagen, DNA, or some 
other material that will really tell us something about the organism from 
which it came. Even plant fossils are mostly carbon and hydrogen when we 
find them, and the thin black films don't tell us a whole lot about the 
organisms that we can't learn simply by examining the fossils visually. 

The most famous example of a fossil that contains well-preserved organic 
matter has to be the frozen mammoths that have been found in northern 
eurasia. These fossils are 10,000 years old or more, and most 
paleontologists consider them to be true fossils, even though they have 
been preserved by only two processes:  (1) freezing, (2) isolation from 
water and oxygen. Even if you don't want to consider these to be fossils, 
there is preserved structural protein in some fossils from a variety of 
places; some of these fossils are millions of years old. There is organic 
material with fragments of DNA and other biologic chemicals in amber, much 
of which is many millions of years old. These are clearly fossils with 
important organic parts preserved. The organic chemicals are still 
recognizable because they have not been heated too much, and because 
chemicals (especially oxygen) have not been able to degrade them. Also, 
very importantly, bacteria were not able to use them for food. Most organic 
material decays after death, and decay is mostly the process of being 
devoured by bacteria. 

Dinosaur bone. Let's see. First, dinosaur bone is often NOT harder than the 
surrounding sediment. However, dinosaur bone is certainly different from 
the surrounding sediment and therefore can be harder. Only some of the 
minerals in the sediment are mobile (can be readily dissolved in water) and 
these are the ones that end up inside the bone. Also, minerals precipitated 
in bone are in the form of tiny crystals cemented together and to the bone 
itself, which makes the resulting structure rigid and hard. Dinosaur bone 
theoretically can contain organic material, sealed in by the enclosing 
sediment. Why doesn't it? Well, sometimes it probably does. However, most 
of the fossils of animals that contain organic matter are younger than 65 
million years. That is a great span of time, long enough for remnant 
organic matter to slowly decay even if it is almost perfectly sealed away 
from water and oxygen. I do think it is possible that interpretable organic 
remains of dinosaurs will be found, if they have not already been found, 
but preservation of organic matter is much less common in fossils of that 
great age. 

Isotope geology is complicated, but certainly it is true that some dinosaur 
bones will preserve the original ratios of some isotopes. Many fossil 
shells much older than dinosaurs do the same. Again, the key is to isolate 
the fossil from agents of change. If the bone is not affected by moving 
water that can bring in isotopes of carbon, say, then the original carbon 
is what you will find. Because bone is so porous it is easy to alter the 
isotope ratios compared to those of a shell, which is typically much less 
porous.

Well, I hope I have begun to answer your questions. You are interested in 
the science of taphonomy, which is the study of the changes that organisms 
undergo while they become fossils, and after that. It is very tricky 
sometimes to understand everything that is going on, but it can be very 
rewarding too. When we understand the changes that have taken place, then 
it is easier to understand the organism as it was before it underwent those 
changes. 

Good luck, and feel free to ask more questions.

David Kopaska-Merkel
Geological Survey of Alabama
PO Box 869999
Tuscaloosa AL 35486-6999
(205) 349-2852
FAX (205) 349-2861
web site: www.gsa.state.al.us