Naturalism has captured science, such that science is no longer a search for *truth*, i.e. what *actually* happened, but the best explanation consistent with naturalistic philosophy, whether it is true or not.
Edward: Correction, philosophy and theology are a search for *truth* Science is a search for knowledge.
Invoking miracles to explain how we get from “this to that,” adds nothing to human knowledge. Science is an attempt to build on the knowledge we have, to hypothesize and discover connections between things we know. Miracles have no connection except in the supernatural mind of God. They have no explanatory value, they cannot be compared one to another, since each miracle is unique and uniquely inexplicable.
I have explained in previous emails that the genetic “leap” from the common ancestor to both human and chimpanzee is quite small, especially concerning the essential functioning genes. And the “leap” lay within known mutation frequencies of genetic change over time.
If anyone wishes to believe that God kept dipping his finger in the brew over the five-million-year-time span lying between man and chimp and their common ancestor, that is their prerogative to believe thatʼs what God did. Neither is it up to science to prove a universal negative regarding any and all miracles.
But speaking of knowledge, scientific knowledge, what we DO know is that the evidence points to man and chimpanzee sharing a common ancestor approximately five million years ago. The genetic evidence is quite plain on that matter as he himself has pointed out concerning the shared lack of a gene to produce vitamin C and shared retroviral genes in homologous DNA locations in both human beings and chimpanzees. I would add to that the evidence of chromosomal fusion that can be seen in the human chromosome no.2 which certainly has left behind marks inside the chromosome itself of being a fusion of two chromosomes (that are still separate in the chimpanzee lineage).(Article on the Web on that topic, and also on several other pertinent molecular evolutionary biology topics.
We ALSO presently know of over a hundred species of primitive ape, all of whose arms were shorter than modern day apes, and who had some other features such as the lack of a simian shelf in their jaws, that means that modern day apes diverged from the primitive ape form (adding longer arms and a simian shelf in their jaws), while the extinct hominid species that lead in the general direction of man retained some of the basic characteristics of the primitive apes.
We ALSO know that all those species of primitive apes became extinct, as did all the species of hominids leading up to man, and even some varieties of human being became extinct as well, like the Neanderthal, (except of course for the one remaining human lineage which lives today).
In summation it seems to me that those who propound the “Design” must face up to the fact of retroviral and other junk in the DNA, thus the Designer does not “take out the garbage.” The Designerʼs “plan” also includes that of ALL his “Designed” primitive ape species, including ALL of his hominid species and even a sub-species of man (Neanderthal), ALL except the one lineage leading to modern man, becoming extinct.
The facts certainly seem to imply that we are dealing with either a “Divine Tinkerer,” or neo-Darwinism. And in the end, just how far apart is the “Divine Tinkerer” hypothesis from that of neo-Darwinism, and so what exactly is the “fuss” about, i.e., concerning the difference between “progressive creationism” and a “neo-Darwinistic evolutionary viewpoint?” There are fine-tuner Christians who see no “fuss” concerning the difference. In fact, fine-tuners agree that it would be more proof of “Design” not less, if life were found elsewhere in the cosmos, on other planets, in other words, if evolution was a cosmic phenomena, rather than say, limited to “progressive creation” on one tiny planet in the entire cosmos.
The view of fine-tuners is simply this, that a God who can design a cosmos that makes people out of billion year old carbon is more of a marvel maker than a God who has to keep pulling rabbits out of his hat and adjusting things. (Reminds me of the way folks, including Newton, used to invoke God as a cosmic repair man who they believed stepped in to set right any minor perturbations in the courses of planets and stars. But today nobody invokes God to do such a thing.)
Quotations From Recent Articles That Bear Directly On Everything I Wrote Above
Chimps Belong on Human Branch of Family Tree, Study Says
John Pickrell in England
for National Geographic News
May 20, 2003
Derek E. Wildman, Goodman, and other co-authors at Wayne State argue in their new study, published today in the journal Proceedings of the National Academy of Sciences, that given the evidence, itʼs somewhat surprising that humans and chimps are still classified into different genera. Other mammalian genera often contain groups of species that diverged much earlier than chimps and humans did, said Goodman. “To be consistent, we need to revise our definition of the human branch of the tree of life,” he said.
Goodman and colleagues used computer methods to analyze the amount of similarity between 97 important human and chimp genes and as many of the same gene sequences as are currently available for less-studied gorillas, orangutans, and Old World monkeys. The results suggested that within important sequence stretches of these functionally significant genes, humans and chimps share 99.4 percent identity. (Some previous DNA work remains controversial. It concentrated on genetic sequences that are not parts of genes and are less functionally important, said Goodman.)
Using the DNA data, the researchers argue that humans and chimp lineages evolutionarily diverged from one another between five and six million years ago.
What does the mouse genome draft tell us about evolution?
by Alec MacAndrew
An astonishing 99% of mouse genes turn out to have analogues in humans. Not only that, but great tracts of code are syntenic—that means the genes appear in the same order in the two genomes.
The findings of the draft mouse genome are astonishingly powerful evidence for common ancestry, mutation and selection: in short for the Theory of Evolution. There is a list with links below for the key points within the paper which can only be explained by evolution. It is just not possible to explain what we see in the two genomes if they have only been in existence for 6500 years unless we invoke deliberate deceit on Godʼs part.
90.2% of the human genome and 93.3% of the mouse genome lie in conserved syntenic segments
The syntenic blocks have been re-arranged by chromosomal events over time The distribution of size of the syntenic blocks is consistent with a random mechanism for chromosomal rearrangements
It is possible to recognise the difference between repeat sequences that were added to the genomes before divergence of mouse and man lineages and those added after divergence
The measured mutation rate since divergence of mouse and man is ample to explain the divergence of the species
The rate of insertions of repeat sequences as a function of time can be measured for both man and mouse
Repeat sequences are tolerated in the same regions in mouse and man and in both cases insertion of repeat sequences is not tolerated in functionally critical regions such as the homeobox clusters
Two sorts of pseudogene exist in eukaryotes—processed and unprocessed—we know how they arise and it has taken millions of years for the pseudogenes we see in mouse and man to arise
Pseudogenes can be identified by the ratio of synonymous to non-synonymous mutations occurring over millions of years and by the fact they do not generally have a homologous gene in the same syntenic position in the other genome
99% of mouse genes have homologues in humans and 96% are in the same syntenic location
The fact that mouse and human are relatively closely related allows us to study orthologous genes—genes which have arisen and diverged from a common ancestor
12,845 orthologous gene pairs were found between man and mouse (homologous genes in the same syntenic location)
The Ka/Ks ratio (ratio of non-synonymous to synonymous mutations is = 1 in neutral regions and the median value is 0.115 in genes)—this can only be explained by common descent
Within genes, regions containing known domains have a lower Ka/Ks ratio than those that do not
The percentage of cases in mouse where the mouse gene matches the most common human allele at sites which have Single Nucleotide Polymorphisms is very close to the percentage of amino acid identity across the two genomes: very strong evidence for common ancestry
Expansion into gene families has occurred in cases where the family has important functionality specific to a lineage
The Ka/Ks ratio in lineage specific gene families is higher than average suggesting that they are undergoing more rapid evolution than the rest of the functional genome as evolution theory would predict
The percentage nucleotide alignment across the whole of the mouse and human genomes (about 40%) is compatible with what is known about the rate of DNA deletion in the two lineages since divergence
The rate of substitutions in ancestral repeat sequences in non-coding DNA is the same as the rate of substitution at four fold degenerate sites in functional regions—very strong evidence for mutation and selection over a long time
The detail of which parts of the genome are more highly conserved between the two species aligns well with functionality
Introns are conserved no more than background non-functional DNA and so do not appear to have functionality in their code
Gene structures—number of exons and coding length in exons—is strongly conserved across mouse and human genomes—very strong evidence for common ancestry
The difference in mutation rate (obtained by comparing mouse and human genomes) between X-chromosomes and autosomes can be explained by what we know about differences in mutation rate in male and female meiosis and relies on common ancestry and mutation over millions of years