I'm making this long post because you seem reasonable, and I think sincere--somewhat rare in those who defend evolution.
I did not "acquire the notion that evolutionary theory is about origins. After all, it all derives from a book named "Origin of the Species," in case you have forgotten. If creation is denied (which it is by me) and life has a beginning, (which is doubted by me) whatever else the evolutionist is interested in, he must assume that life originated somewhere, somehow, and however much he'd like to avoid the subject, the origin of life is central to the whole quesion of evolution.
Quickly I'll address some points you made:
1) mass extinctions of species (more species have lived and perished than currently exist)
Extremely doubtufl, and at least unproveable.
2) embryonic development in higher life forms exhibits stages in which archaic, biologically useless characteristics manifest, such as tails and gill slits in human embryoes.
This is very old and almost universally repudiated.
3) Parallel evolution, as with crocodiles and alligators, two distict species that are nevertheless remarkable similar and well-adapted to survive in similar environments. Or were those Florida alligators here all along, BEFORE the land subsided into the Carribean Ocean, just waiting (out in the desert or in the forests?) for the ideal environment to evolve? How did they survive in the meantime?
Interesting question, "how did they survive." It is interesting because those who reject the creation story (or deluvian story of Noah and two of each species) are quite right in observing, if there are only two of a breeding species that odds against survival are zero to none. Yet, if evolution is right, each new species had to begin with at least one new breeding pair. Since the only known way a new species could develop is by mutation, that would mean the exact same mutation would have to occur in at least two offspring of some creature to make breeding of the new specie possible at all, and for survival, would require a larger number of breeding pairs, all with the same genetic characteristics produced by mutation at approximately the same time. Since there are millions of species, this event would have had to happen millions of times.
In all of recorded history there is not one example of a mutation that has produced a new specie, and, with the exception of some extremely doubtful cases, there has never ever been one mutation of any creature that was beneficial.
Now, with apologies for it's length, I'm going to provide a very long argument against evolution by a micro-biologist who is neither a creationist or "intelligent-designist" but simply recognizes that evolution is nothing more than a very unsubstantiated hypothesis that is interesting, and may ultimately be valid but is a long long way from being established and has no basis for being taught as science at all.
The so called “theory of Evolution” was first proposed by Darwin based on observable, physiological characteristics. This was seized upon as an escape from the dominance of religious thought, which had held that man was a being made, and thus owned, by a mystical God.
Some fossilized remains of human-like bones were found, and the “flow-chart” constructed which fitted the theory. Basically, the theory was, in order to explain similarities of form across specie, the various species must have had a common ancestor and then “diverged” in small but cumulative ways. It was a neat story. And there are some small ways it does work - but only within species. As an explanation for the variety of species, and for the origins of the existence of man, it is ultimately wrong.
The fossil record theory of evolution had to rely on a few scattered bones for its evidence. Collected from geological strata dated back 4 million years, very little – relatively speaking - has been discovered the majority of which are scattered bones from which final body shapes have had to be reconstructed. The evidence is scanty. However, with the discovery that the genome was the conveyer of hereditary material, came the “link” that paleontologists were looking for. DNA carries the information for the amino acid content of proteins and triglycerides of lipids which make up the enzymes, organs and structure of the body. Minor physical variations which were passed on to offspring within species were discovered by Mendel, and rediscovered in the early 20th Century (Mendels’ work was largely ignored since no-one could understand it, and it was assumed to be either wrong or faked – an attitude which persists to this day!!). Using simple crosses, these variations could be linked to genome diversity, later discovered to be variations in DNA content and information.
This is where the major error was made. Information regarding genetics was linked to known anatomy and physiology, and assumed to be direct. In other words, the gene provided the information for the structure of the human form, different humanoid forms had been found and posited to have arisen from previous forms, with humans and apes having arisen from a common ancestor, and all animal life having sprung from the same set of cells and with accumulated random error in the DNA inherited by offspring the means.
How do genomic variations occur?
1. Point mutation. This is when damage to the DNA from external sources such as radiation, or cellular aging, the DNA changes one of its base pairs, thus changing the code from one amino acid to another. Almost always this is deleterious.
2. Recombination. This occurs when DNA from one part of the genome breaks away and rejoins at another part of the genome. It is more regularly and frequently an event in all genomes, prokaryote and eukaryote, as small sections of DNA are exchanged between chromosomes during the phases of cell division, usually being either neutral in effect or deleterious as in Philadelphia 21, which leads to Chronic Myloid Leukemia.
3. Transposition. Small fragments of DNA known as transposons are able to “lift” fragments of DNA and transport them, in the case of bacteria into a different cell via plasmids and viruses, or in the few eukaryotes found to have them ie. Drosophila, around the cell genome.
4. Re-assortment. Possession by eukaryotic cells of two pairs of genetic information which separate randomly in cell division and then pair with the opposite from the second parent during fertilization.
Which type of genomic variations are important for evolutionary theory?
Since evolution posits that changes are acquired and passed on to offspring, only changes in the germ line DNA, ie sperm and ova, have any significance. Changes to somatic cells are irrelevant to the theory.
Thus, the unit of significance is not time, but generations.
Prokaryotes (Bacteria).
Bacteria have been studied extensively for years. They have a single, looped genome, which has been fully analysed. With a short life span [E.col) under optimal conditions reproduces in 20 mins] they are ideal for examining generational changes. Many can swap DNA very fast, as the spread of Antibiotic resistance genes demonstrates. In spite of years of treatments and environmental changes, alterations to genomes, spread of genes via phages, plasmids, transposons, no bacteria has ever shown any sign of any characteristics of anything but itself. Even bacterial types, eg. Staphylococcus, Tuberculus, streptococcus, don’t change into one another.
Eukaryotes – multi celled organisms
The most extensively studied eukaryote is the fruit fly, Drosophila melanogaster. With only 4 chromosomes and a reproductive cycle of 7 days, they have made an excellent tool for investigation. Used since 1910, when T. H. Morgan first started modern genetics with them, we have been able to study 4,940 generations. (If we assign 15 years as an arbitrary generational time for humans this is the human equivalent of looking back 74,100 years).
Drosophila, over this time have been exposed to just about every sort of mutant generator. Mutations have been found for almost all characteristics, the wings, colour, eyes, thorax components, and many more. Certain genes that convey rapid mutations have been isolated. Drosophila come in every wing shape (including wingless), colour and twisted up contorted variety. But in all this time, they have never shown any indication of being anything other than D .melanogaster.
There are reasons why Drosophila is more likely than humans to express an evolutionary change – they have less DNA to be changed. With only 4 chromosomes compared to humans 22, there is a smaller “target” area.
Morever, they have transposons, which can move DNA rapidly around the cell. Humans have no transposons, and have to rely on point mutation, re-assortment and recombination. However, there is even here a difficulty. Females form their ovaries and ova while they are still themselves embryos. At birth, all of a females reproductive capacity is already “in place”. Ovaries are buried deeply, not easily exposed to environmental assault, and each ova has partially completed its cycle to final stages of release ready for fertilization. We are on a better chance with males, whose sperm are made freshly and frequently, in very large amounts, and whose organ of construction is more exposed to the environment. But this means the chances of genetic mutation are halved to only one of the two needed to produce new generations.
Further problems are encountered when considering that:
Most mutations are deleterious, those that are not are usually neutral (i.e. brown eyes to blue)
Because only one parent will be carrying the chance arisen genetic variant, it must be dominant in its expression, ie. It is expressed in the phenotype in preference to the original gene carried by the other non-mutant bearing parent. In most cases, the mutant form is recessive (again, blue eyes to brown).
There is a dilution effect. Down generations, a single mutation, which may gain expression in 100% offspring in the F1 cross, will gain less expression in the F2 as the offspring reproduce with partners without the mutant form and genetic reassortment of chromosomes will produce offspring not carrying the mutant variant.
From plants, prokaryotes, simple single celled organisms, and on, studied extensively, forcibly mutated, crossed and re-crossed with selected mates, the only variation ever seen is always within the species. No specie has been seen to change into the beginnings of another.
The theory claims that the selective pressure for a species to change is survival.
However, the problem with this is that species survival is directly related to the ability to produce more offspring in the face of the challenge. This means that a change has to occur quickly, yet the theory states that changes are slow, over millennia.
If the theories claim that changes occur but lie dormant until selection favours them, we have to ask how and why changes of complexity which require the entire change to be present occur, and why should they, when the organism was obviously surviving well enough. An example is that of certain insects which when clustered look like a flower. Co-ordinated changes all must occur at the same time, for each insect which carries the different colours and shapes to produce it’s part of the jigsaw. Given that the insects were obviously surviving well enough to produce these changes – slowly over time according to the evolutionists, we have to assume they were surviving well enough as they were in order to have got to this point. So, why would they change, and how would such a complex change occur by “random mutations”?
The issue of complexity is knotty problem for classical evolutionists. Quite apart from the frequently cited case of the mammalian eye, all aspects of which needs to be in place to work, we can simply consider that of the working cell itself. Let’s look at DNA transcription to produce a protein. The correct DNA sequence must be in place. The mRNA must have been produced correctly by it’s DNA, and be in place, the tRNA - a different one for each amino acid – must have been correctly transcribed and formed, the ribosome - both units, must have been correctly transcribed and its tertiary structure formed, the enzymes involved must all be present and active. The ATP pump must be working to provide the energy required. The correct solution of salts and trace elements must be present and at exactly the correct pH.
And this is just to form one simple protein. To suggest a small change in one gene can bring about major changes in the face of such complexity beggars belief.
But there is another major problem which those who linked genetics to paleontology seem not to understand.
To return to the protein, once all the amino acids are linking into the chain, this is only the first stage. The protein then takes a tertiary conformation. Almost all proteins form and alpha-helix. Since a helix can twist right (d) or left (l) in theory this could be either. In fact, apart from a very few rare instances, all proteins are left helices. This tertiary folding is dependent, not only on the amino acids being present in the correct order, but the molecular shape and charge of the amino acids, the liquid environment the protein is floating in, and the presence of various trace elements and minerals. Since all proteins take a (l)-alpha helix, we are left facing the conclusion that the shape, the three dimensional attribute, is something which the environment the protein is in forces on it, and that there is only one shape available to proteins because of this constraint.
The issue of tertiary structure is found in DNA, which is not linear, as the diagrams represent, but forms a twisting, twisted and twined shape manipulation of which is essential for genetic transcription and recombination to occur.
Which brings us to Developmental Biology.
Developmental biology is that area of biology which asks, what makes the final body shape. Why an elbow? How come a knee? What rounds a heel, gives a liver the exact shape and conformation it does. And the answer is, we don’t know. We do know of certain complexes of gene groups which contribute certain factors involved in the skeleton, largely because of the altered effects seen when the genes are altered. The products of some of these genes, acting in concert with a multiplicity of other factors, does play a part in at least providing the cellular components required to form a developing limb bud, cranium and jaw structure. However, many of the experiments which claim an ‘effectiveness” are simply noting the presence of an essentially toxic compound useless to the body, and a malformation, as the Hox1a gene associated with slightly mal-formed hands and feet of those carrying the variant (very very rare). This doesn’t, of itself, prove the Hox box does in fact control limb structure, since the product of the mutant gene is a shortened form of the required protein, therefor unrecognisable to the bdy and possibly treated as many other toxic elements are and consigned to the furthest limbs. However, other more positive evidence, does support the contention that the Hox box provides some of the requirements for limb bud formation in the developing embryo up to the 12 week gestation. However, although it provides the limb bud, there is no evidence that this directs and controls the final shape, ie the anatomy of the limb.
There is no genetic evidence which demonstrates the final skeletal form is purely genetically driven. And the skeletal form is the basis of all of paleontology. The evolutionists are in fact basing their entire "theory" on a mistaken link - that of genetics with skeletal form.
Ultimately, there is far too much complexity to the living cell, plant and animal for single changes to do much other than contribute to likely elimination of the indivual carrying the mutation. To suggest a single mutation can so affect an entire species is like suggesting that the fruit seller at the gates of a vast and complexs industrial city can significantly affect the entire city by altering where he is standing by a few feet.!!
An alternative speculation to Intelligent Design and Evolution.
It is stated by scientists today, that either humans “evolved” from previous, different animals by random mutations in DNA, or we were made by a God. It is never considered that both may be wrong, and there could be other explanations for speciation, a different explanation for the “fossil record”. This is due as much to the blind almost religious fervour of evolutionists as to the same religious dogmatism of the creationists. If one does not accept that something is possible, one does not, after all, go looking for it.
I would like to propose that it is perfectly possible that the reason shape is largely conserved across species, and has stayed so for millions of years, is the same as that which directs tertiary formation of proteins. That it is a combination of factors, including the environment which the forms develop in, which directs the final shape, and that the shape found in all animals, (with a series of minor variations) is so, not because of “descent” from a common ancestor, but because in the environment of this world, it cannot take another. That the fact that this is a water and air based planet, that all living things are made of carbon, with some hydrogen, nitrogen and oxygen thrown in, the combination of molecular shapes and charges, pH, salts, trace elements and minerals, water, temperature, gas pressures and many more, combine to effect the developing animal such that the final tertiary structure cannot be anything other than what it is, and which in almost all cases conforms to the same basic shape.
I suggest that the animal forms we see now have always existed as they do, but have minor variations within species, which can arise from a variety of sources, largely genetic recombination, and which has the effect of allowing specie continuity in the face of minor environmental changes, such as the case of pale and dark moths on trees darkened by industrial smoke pollution.
There is one final point. The fossil record is not as sequential as paleontologists represent it. Fossil remains have been found “out of sequence” in the time scale and are either ignored or written off as “aberrancies, or washdowns”.
And fossil remains have been found in strata dated at millions of years old; they are identical to Homo sapiens sapiens. That is, us. A flat contradiction of the “fossil record” and evolution and which never gets adressed by evolutionists. Wonder why??
The evidence against evolution, to my mind, is much more convincing than the evidence for it. Today, anyone who takes that position in academia, or even in science, will be branded a creationist or "intelligent-designist" or something worse. Evolution is the accepted "religion" of the day, and whoa to anyone who questions the accepted orthodoxy.
Hank