"
You full well know that this is not true. We do not have any such complete set of intermediate forms. Further, the only connections made between the fossils we do have are those imagined by interpreters of this data."
I did not use the word "complete." There is no such thing. You cannot possibly imagine ever having every fossil. But we do have a pretty good record of human evolution. Are you familar with all of these?
Sahelanthropus tchadensis
Ardipithecus ramidus
Australopithecus anamensis
Australopithecus afarensis
Kenyanthropus platyops
Australopithecus africanus
Australopithecus garhi
Australopithecus aethiopicus
Australopithecus robustus
Australopithecus boisei
Homo habilis
Homo georgicus
Homo erectus
Homo ergaster
Homo antecessor
Homo heidelbergensis
Homo neanderthalsis
Homo sapiens
And maybe you have read about the latest find, from Spain, Pierolapithecus catalaunicus.
Now, which of these do you have a problem with? Which of these do you think are fully human and which do you think are completely non-human apes? Make your choices.
But you have a bad choice. Let's take the most human-like non-human on the list. If you say the Neanderthals were human, then I am going to pull out the genetic testing that shows that they are not and I will start pointing out all the physical traits they have that no extant humans have, such as brow ridges. If you say they were not human, then I will point to their sophisticated life with tool making and burying dead and all that. If you make your break at a point further in the past then I will have an even easier time with you.
A few other things.
"Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees," Chen FC, Li WH, American Journal Human Genetics, 2001 Feb;68(2):444-56.
I want to look at pseudogenes can be used to trace the evolutionary history of apes. For this paper, they used "53 autosomal intergenic nonrepetitive DNA segments from the human genome and sequenced them in a human, a chimpanzee, a gorilla, and an orangutan." These segments included "Y-linked noncoding regions, pseudogenes, autosomal intergenic regions, X-linked noncoding regions, synonymous sites, introns, and nonsynonymous sites."
When all the various sequences are considered as togther, they "supports the Homo-Pan clade with a 100% bootstrap value." This is pretty clear evidence of the shared common ancestor for humans and chimpanzees.
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The next subject I wish to explore here is chimeric retrogenes. They happen to be functional but they arise in a specific way that allows them to be used to trace evolutionary family trees.
The basics are that mRNA is turned into cDNA through reverse transcription. This sequence is then permantently integrated into the genome by endogenous integration proteins.
The evolution of the primates and apes can then be traced by when specific sequences were integrated into the genomes of the various common ancestors.
When looking at this 12 specific chimeric retrogenes, you get the following chart.
http://nar.oupjournals.org/cgi/content/full/31/15/4385/GKG496F3
The distribution of the various genes in the various primates and apes, including humans, matches that which would be predicted through other techniques. That this technique matches that as done by other genetic, molecular and fossil methods is a very powerful combination of factors that strongly indicate the descent of humans from a common ancestor with the other apes.
"The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination," Anton Buzdin*, Elena Gogvadze, Elena Kovalskaya, Pavel Volchkov, Svetlana Ustyugova, Anna Illarionova, Alexey Fushan, Tatiana Vinogradova and Eugene Sverdlov, Nucleic Acids Research, 2003, Vol. 31, No. 15 4385-4390.
http://nar.oupjournals.org/cgi/content/full/31/15/4385
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The next subject to look at is retroviral DNA insertions.
"Constructing primate phylogenies from ancient retrovirus sequences," Welkin E. Johnson and John M. Coffin, Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, Issue 18, 10254-10260, August 31, 1999.
Here, about a dozen different retroviral DNA inserts are used to construct the evolutionary tree of human and the other apes and primates. See the following chart to see how closely the different inserts match.
http://www.pnas.org/content/vol96/issue18/images/large/pq1892815002.jpeg
The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage. Most HERVs are nonfunctional, selectively neutral loci. This fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as phylogenetic markers.
...
Endogenous retrovirus loci provide no less than three sources of phylogenetic signal, which can be used in complementary fashion to obtain much more information than simple distance estimates of homologous sequences. First, the distribution of provirus-containing loci among taxa dates the insertion. Given the size of vertebrate genomes (>1 × 109 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14). Furthermore, integrated proviruses are extremely stable: there is no mechanism for removing proviruses precisely from the genome, without leaving behind a solo LTR or deleting chromosomal DNA. The distribution of an ERV among related species also reflects the age of the provirus: older loci are found among widely divergent species, whereas younger proviruses are limited to more closely related species. In theory, the species distribution of a set of known integration sites can be used to construct phylogenetic trees in a manner similar to restriction fragment length polymorphism (RFLP) analysis.
Emphasis added.
http://www.pnas.org/cgi/content/full/96/18/10254
There are many such papers out there using LTRs to trace evolution. Here is another.
Liao, D., Pavelitz, T., & Weiner, A.M. (1998). Characterization of a novel class of interspersed LTR elements in primate genomes: structure, genomic distribution, and evolution. JMolEvol, 46, 649-660.
Phylogenetic analysis of the LTR13 family confirms that it is diverse, but the orthologous U2-LTRs form a coherent group in which chimpanzee is closest to the humans; orangutan is a clear outgroup of human, chimpanzee, and gorilla; and baboon is a distant relative of human, chimpanzee, gorilla, and orangutan.
And another...
"Evolutionary implications of primate endogenous retroviruses," Shih A, Coutavas EE, Rush MG,
Virology. 1991 Jun;182(2):495-502.
In the second study, a comparison of endogenous proviral DNAs and their adjacent sequences has been used to analyze the evolutionary history of three previously reported human endogenous retroviruses, HERV-E(4.14), HERV-R(3), and HERV-Ia. It is shown that these retroviruses have also been resident in the primate line since before the ape-Old World monkey divergence.