The scientific method is the only prerequisite for understanding why evolution is the accepted pathway to animal and human existence. I will refer to it during this document so a brief explanation may be in order.
The scientific method relies upon several phases. Firstly observations are taken of the phenomena under study, secondly an hypothesis is established which fits the phenomena observed, the hypothesis must have three distinct characteristics aside from its conformance to observation. It must be verifiable or repeatable, in other words if others make the same examination they must agree that the hypothesis does fit the observations. It must be falsifiable, meaning that it must be possible to carry out an experiment, if not now then in the future to check its conformity with observation. It must only use as accepted facts those theora which have yet to be found flawed. Any hypothesis that follows all of these criteria can be entered into the literature, the current 'body' of knowledge.
All of these are under potentially constant attack and there are two ways in which any hypothesis may be removed from the understood science. An observation may be made which does not fit the hypothesis forcing it to be modified. A new experiment may be devised which allows the hypothesis to be proven untrue, in effect this falsifies the hypothesis.
Since its inception, almost 150 years ago no theory has been attacked with such consistency and longevity as evolution, in fact nothing has inspired so much controversy since the heliocentric view of what we now call the solar system. Despite this the debate effectively was over by the turn of the century, all competing arguments had been destroyed a century ago. Since then evolution has been accepted as fact and every experiment to test it adds more weight to its power. Now it is entirely fair to say that there is no controversy at all. The entire scientific community accepts evolution, indeed without it much of what we've learned about life on Earth is based entirely on these understandings. This is not to say that scientists agree on the details, there is still fierce debate on a number of subjects, but only a few religious organisations are now shouting about a lost cause and trying to find flaws in a theorem which explains every phenomenon since observed.
The definition of evolution (in a biological sense) has changed over the nearly two hundred years it has been in usage, in fact given the manner in which science works, it would be amazing were this not the case. Currently it is defined by biologists as being a change in the expression of alleles over time. That is a change in the phenotype of descended organisms over their ancestors. This is also known as microevolution.
All of the sources I've examined accept that this microevolution takes place and that the driving force behind it is the modification, through some means of the chromosomal nucleic acid which forms the pattern of the developing organism and holds the key to its complexity.
In practice, the debate we are embarking upon is based on a slightly different concept. It is my belief that I can demonstrate a plausible mechanism for life to evolve from its simplest early organisms to the biodiversity we see today. This submission is my attempt to do this.
In the simplest term's speciation is the point at which the physical (phenotypic), biochemical (genetic) or behavioural divergence of two independent populations of a single 'type' or species of organism becomes expressed in a readily observable fashion. In naive terms this could mean an inability to interbreed but in practice it could be related to divergent behaviour or even modified anatomy.
Speciation is not a theory, it is demonstrable in the laboratory and has been observed a number of times in the wild. Sometimes this is caused by two genuinely divergent species interbreeding (the reason this is no longer used for the definition of a species as it doesn't formally relate to many of the species we see around us, particularly plant species). On other occasions a mutation spontaneously occurs or behavioural selection takes place in the environment.
The diversity of life we see around us implies either directed control over the appearance of species (in either the short or long term) or a long term process consisting of some form of selection.
I intend to demonstrate why only one of these solutions explains the observed world.
There are two major means by which diversity is achieved within a population. Firstly the transcription process during cellular meiosis generates a small percentage of errors, the vast majority of these have no immediate effect. Some have a catastrophically bad effect but a larger number cause general variation in the performance of a population in a variety of ways all of which add to its ability to survive environmental or behavioural change. The second method is sexual reproduction itself. Broadly, this allows for a thorough mixing of the genetic heritage of the parents into a new, unique, genetic structure for the offspring, both these are easy to demonstrate in the laboratory and the understanding of the mechanisms involved began with Mendel's work long before Darwin published.
Three major discoveries this century, all within a few years of each other described the major mechanism for evolutionary change. Shargaff published his studies on base pair equivalency using paper chromatography, then in 1953 Crick and Watson published the seminal biochemistry paper in the journal Nature. In it they described the structure of DNA. A short while after this Crick independently developed his 'wobble' hypothesis that explains the manner in which life chose to convert the mathematical properties of the DNA molecule into protein structure. Subsequent discoveries have described the process in fine detail and also make it abundantly clear how such a structure could have formed through evolution. In fact once you see the mechanism it is apparent that only through iterative modification of the process could such a system have come about.
Life on Earth is roughly 3.5 billion years old, and it began with a simple organic molecule called a replicator. We don't know what type of molecule it was but it bred quickly, making copies of itself, identifying through random events the most successful combination of structures and producing those until the seas heaved with them. This is the true progenitor of all life on Earth.
Life is actually defined by its proteins. Every living thing relies upon them to do the actual work of a cell. If DNA is its memory and RNA its brain then the proteins are its muscles. Proteins demonstrate an evolutionary adaptation as well. While it is not possible for proteins themselves to pass characteristics on to future generations, those generations will have proteins that are slightly different from previous collections. It is possible to trace a complete evolutionary path by using proteins alone, it conforms exactly with the genetic evolution and extremely closely with taxonomic studies. It is a powerful set of corroborating evidence for the evolutionary pathways we know and, in addition, adds weight to the approximations of the time life began on Earth. Specifically, the rate of change can be measured and from it can be seen roughly how long evolution takes to get from one form of life to another this conforms closely with the fossil record.RNA is a similar molecule to DNA and has several interchangeable functions. In higher life forms RNA operates in two main roles in protein production. A strand of RNA called 'messenger' RNA is patterned on a portion of the DNA strand and then acts as a pattern for the protein. A second form of RNA called 'transfer' RNA accepts amino acids and matches with triplet groups on the mRNA to form the sequential chain of proteins. In order to make the process simpler, complex structures known as ribosomes have developed which speed the process and reduce the errors inherent in the mechanics of the system. In fact, errors in translation are almost unheard of in comparison to errors in transcription. There is an evolutionary bias here, if there was an error in translation then you simply have a slightly different protein, whether it is more or less successful is irrelevant since the change cannot be passed on to the next generation. Organisms have steadily improved their ability to translate accurately as they have evolved but their ability to carry out error-free transcription has changed little for billions of years. This is simply because evolution is a positive influence on a population.
Higher organisms, particularly animals, are extremely complex. Progressively specialised organs have developed to take care of functions for the entire body, not merely for their own cells. This is an inevitable consequence of evolution and relates to the fact that a cell is necessarily a generalist. As soon as multicellular structures become extant, probably in the earliest forms in co-operative ventures in the manner of the Portuguese Man'o'war today, there is an inherent drive to specialisation. Once again the mechanisms by which this happens are well understood and predicted by evolution.
The evolution of creatures is never so clearly demonstrated as it is with developmental biology. In these instances it is possible to see the specialisation process begin and watch it as though you were watching a billion years of cellular alteration.
In all animals there are vestigial structures of one form or another. In humans, for example, there are at least four complete organs with no function. The appendix, ulula, tonsils and coccyx are all redundant now. The reason for this is that adaptations, which are required in one species, fall into redundancy when the species evolves into a new form. Unless their presence confers some specific and significant disadvantage in the new configuration the vestigial organ may remain for a very long time. This certainly implies development rather than creation, there are also examples, classically the 'Panda's Thumb' popularised by Stephen Jay Gould, of jury-rigged, poor or inefficient structures. If the organisms were designed these would presumably not have been included. In human evolution the classic is the urethra - prostate system, a seriously flawed mechanism which causes a multitude of problems amongst adult men.
From the beginning of serious studies this issue has caused controversy. In fact the currently accepted figure didn't become so until this century. While the final figure is arrived at by the use of radiometrics it is bounded by figures based on entirely different means. The oldest it can be is set by the age of the universe which is a figure quite easily calculated by looking at the rate the corpuscular structures of the visible universe are diverging. It is discovered that the distance between any two corpuscles is directly proportional to the rate of increase of that distance. This feature can only be observed if the corpuscles are traced back to a single point which is arbitrarily small. The mathematics gives a figure of approximately 13 billion years since the birth of the universe.
The Earth, by definition, is not so old. Equally there are structures which are of a minimum age. The Antarctic icecap has seasonal layers, at least 2.4 million of them, setting a minimum age at 2.4 million years. The silt deposits of the Niger River can be used to set a lower bound of 45 million years. Calcification rates in fossils prove ages out to approximately 500 million years. Stratified rock can be used to prove values out to a billion years or so. By the examination of metamorphic rock it is possible to set an age of around 4.5 billion years. Geologists now date the Earth at 4.55 billion years, a date derived for a number of reasons.
This subject is still under debate. Recently two facts were observed about space. It is observed that intrinsic in space is the creation of quanta of energy. In addition it is clear that in space energy can be spontaneously converted into mass and that there is an inherent imbalance in the ratio of matter and antimatter so generated. These discoveries are still fairly new and there is a great deal of work being undertaken to find out what contribution this would make to the big bang but the research is very interesting.
The methods of dating finds are quite varied. In practice the finds can be dated by placing them in a construct called the geologic column. There are a number of complete geologic columns around the world but in most locations a subset of this has to be used. The subset merely has to be placed into the column in the correct place. There are a number of tracers that can be used. Major meteorite impacts leave characteristic traces in the strata around the world that contain the same rare elements. A largely iridium layer appears at the K-T boundary which has encouraged a number of theorists to suggest the size and consistency of the layer indicates a huge impact which may be implicated in the large K-T extinction, one of the largest in the record, roughly 65 million years ago. Based on evidences such as these, the column can be reconciled with the fossil record and once fossils have been located into the column then the fossils can be used later to find the position in the geologic column for other sections, particularly when they are small sections. Trilobite fossils are extremely ubiquitous for one section of the column, absent elsewhere, dinosaurs are particularly useful as, for example, sauropods are almost exclusively Jurassic, ceratopsians and dromaeosaurids largely Cretaceous and so on.
Undoubtedly the principal tool used in geologic dating is radiometrics. Wherever possible several different methods are used and they almost always agree to within very small variations. The evidence for the age of the Earth is almost indisputable now.
Fossilisation takes a varied amount of time depending on conditions. Some classes of object can become fossilised in as little as five to ten thousand years others can take at least an order of magnitude longer. Fortunately calcification is a much steadier process. Calcification starts as soon as fossilisation is fully underway but it doesn't complete for at least 250 million years. This gives us an opportunity to make use of this feature in assisting with dating.
The evolutionary pathways are complex but there are a few very clear examples that allow easy relationship between fossils found in the same stratum. The classic example is the flowering plant. From our perspective today it seems strange that there were no flowers in the world long ago. Suddenly, at the end of the Jurassic era there was a dramatic change in the vegetation in the world. The first flowers appear to have been grasses but within a few million years there were a huge variety. Flowers allow much more rapid sexual reproduction and with the use of wind, insect vectors and so on a much wider distribution allowing plant populations to cover a wider area and therefore the gene pool can be much larger. Though this was developed to aid the plants in question it created a niche for animals to exploit as well. A whole new class or low browsing dinosaurs appeared to take advantage and following them a collection of carnivorous dinosaurs dedicated to breaking up the new larger herds which were now practical because of the density of the foliage. The fossil record, of course, supports this course of events, no other explanation has yet appeared which does.
While flowering plants may be the most famous example of taxonomic change across the record there are others. To describe them would take too long but for a few examples look at the sudden explosion of land-dwelling amphibians, the rapid expansion of mammals, the localisation of marsupials, the supremacy of placental mammals and the rapid use of the avian frame to exploit flightless niches.
Despite the repeated attacks on evolution it has remained unassailable thus far. The entire scientific body accepts evolution as fact just as they accept that the sun is a star and black objects don't reflect light. This is impossible unless the evidence has failed to prove any irreconcilable problems with the theory and there is significant supporting evidence.
In order to replace evolution with a 'young Earth' creation model you must demonstrate that all of developmental biology, geography, physics, geology and much of chemistry are all fatally flawed. I have seen nothing that suggests to me that this is possible.
This has been a brief introduction to how evolution fits into the scientific 'roadmap'. I have decided not to include a full bibliography, however, the principal references and authors covered in this are as follows:
Crick, Francis: What Mad Pursuit Crick and Watson: Original letter to Nature 1953 Darwin, Charles: The Origin of Species Dawkins, Richard: The Selfish Gene and The Extended Phenotype Gleick: Chaos Gould, Stephen J: The Panda's Thumb and The Urchin in the Storm and Adam's Navel Maxwell, James Clark: Scientific Papers Perutz, Max: Is Science Necessary? Stryer: Biochemistry Watson, James D: The Double Helix