Why r evolutionary educators/scientists suppressing dissent?

[Bart007]

> Meet the ID's latest martyr, Guillermo Gonzalez.
> From the article:
> ---------------------------------------------------------------------------­­­--------
> Leading proponent of theory targeted by atheists,

Dr. Guillermo Gonzalez is an Assistant Professor of Astronomy at Iowa State University (ISU).

Credentials: Born in Havana, he and his family fled from Cuba to the United States in 1967, where he earned a Ph.D. in Astronomy from the University of Washington in 1993. Author of nearly 70 peer-reviewed scientific papers and co-author of a major college-level astronomy textbook, Dr. Gonzalez’s work led to the discovery of two new planets, and he has had his research featured in Science, Nature, and on the cover of Scientific American. He is building new technology to discover extrasolar planets. He served on the NASA Astrobiology Institute Review Panel in June 2003, and the National Science Foundation Advanced Technologies and Instruments review panel in January 2005. And He has served as a referee for Astronomical Journal, Astronomy & Astrophysics, Astrophysical Journal (and Letters), Icarus, Monthly Notices of the Royal Astronomical Society, Nature, Naturwissenschaften, Publications of the Astronomical Society of Japan, Publications of the Astronomical Society of the Pacific, Origins of Life and Evolution Biospheres and Science.

The Crime: Dr. Guillermo Gonzalez contributed to scientific Intelligent Design Video 'Privileged Planet'.

The Punishment: Religious studies professor Hector Avalos—faculty advisor to the campus Atheist and Agnostic Society—began publicly campaigning against Dr. Gonzalez and his work in order to “uphold the integrity of our university” by “reject[ing] efforts to portray Intelligent Design as science.” Furthermore, in the spring of 2007, when ISU President Gregory Geoffroy denied Dr. Gonzalez’s application for tenure, despite Iowa State University's Physics and Astronomy Department recommendation that Dr. Gonzalez receive an Associates Professorship.

This followed on the heals of of the attack on the Smithsonian Institutes science magazine that included an article written by Stephen Meyer that supports Intelligent Design ("The Origin of Biological Information and the Higher Taxonomic Categories," which cites mainstream biologists and paleontologists from schools such as the University of Chicago, Yale, Cambridge and Oxford who are critical of certain aspects of Darwinism.) Mr. Meyers holds a Cambridge University doctorate in the philosophy of biology. The article was received by the Institutes Richard Sternberger, who placed the article in the peer review process, was reviewed by 3 scientists, and approved for publication. The powers that be among evolution ideologues from Talk Origins to Academia shed their rage against the Smithsonian for allowing this ID paper to be even sent for peer review, much less be published.

Richard Sternberg in particular came under heavy vicious attacks from outside and inside the Smithsonian prompting him to file a complaint with the U.S. Office of Special Counsel. The Smithsonian issued an apology to evolutionists and promised their magazine will never again publish another science paper that supports intelligently design. And who had not heard evolutionists belittle creationary scientists by claiming their science is so wrong and poor that they can't get them published in major science journals and periodicals.

The U.S. Office of Special Counsel eventually determined that Mr. Sternberg had indeed been discrimnated against, and in a most vicious and unprofessional manner.

Once again the lunatic atheist fringe that control our public education continue to use their power of censorship to control what students, and the public, may hear and think.

1984 has come and past, yet George Orwell's "1984" is alive and well in the hands of atheistic pro-evolutionary thought Police who enforce their evolutionary belief system on an unwary public despite their theory's failings as science.


In our educational systems a few evolutionary agents of the thought Police moved always among them, spreading false rumours and marking down and eliminating the few individuals who were judged capable of becoming dangerous.


And in the general hardening of outlook that has set in, practices which had been long abandoned: Censorship, Ad hominem Attacks, Ridicule, Public Humiliation, A Science established by Authority rather than Evidence and Reason - not only became common again, but is tolerated and even defended by people who consider themselves to be enlightened and progressive. Defenders of THE TRUTH, they seek to eradicate, in their words, "purveyors of Thoughtcrime".


Thoughtcrime was not a thing that could be concealed forever. You might dodge successfully for a while, even for years, but sooner or later they are bound to get you. Creationary scientists simply disappeared, always during the night, in the darkness. Your name was removed from the registers, every record of everything you had ever done was wiped out, your one-time existence was denied and then forgotten. You were abolished, annihilated: vaporized was the usual word.


And if all others accepted the lie which the Evolutionism Oligarchy imposed-if all records told the same tale-then the lie passed into history and became truth. 'Who controls the past' ran the materialists slogan, 'controls the future: who controls the present controls the past.'"


Day by day and almost minute by minute the past has been brought up to date. In this way every prediction made by evolutionism could be shown by documentary evidence to have been correct; nor was any item of news, or any expression of opinion, which conflicted with the evolutionism of the moment, ever allowed to remain on record. All evolutionary science was a palimpsest, scraped clean and reinscribed exactly as often as was necessary.


------------------------

My challenge to those who responded is to provide a strong bit of specific scientific evidence that has clearly lead you to accept evolution as being a scientific fact, as so many of you wantonly proclaim. Please be specific and provide one piece of evidence from science at a time. Be prepared to defend whatever convincing scientific evidence you set forth.


I, on my part, aim to respond, with the hope of demonstrating that: Evolutionism is a fairy tale for grown-ups. This theory has helped nothing in the progress of science.


To wet your appetite, note the following:


Scientists abandoning Evolution


"Scientists who utterly reject Evolution may be one of our fastest growing controversial minorities. ... Many scientists supporting this position hold impressive credentials in science." Science Digest:
`Educators against Darwin', winter, 1979.


In a Newsweek article, 1985, "The great body of work by Charles Darwin is under increasing attack and not only by Creationists, but by all sorts of other scientists." In this same article, one evolutionist stated that "things have gotten so bad in the field of Evolution that I am thinking of moving into a field with more intellectual honesty, like being a used car salesman."


"Today, a hundred and twenty years after it was first promulgated, the Darwinian theory of evolution stands under attack as never before. There was a time. not too long ago when it seemed to the world at large that triumphed once and for all, and that the issue was henceforth closed. And yet, within the last two or three decades the debate about evolution has not only revived but is showing signs of heating up. Indeed, the question whether claims are justified is currently being discussed and argued, not just in fundamentalist circles, but also on occasion in research institutes. and in the prestigious halls of academe. The fact is that in recent times there has been increasing descent on the issue within academic and professional ranks, and that a growing number of respectable scientists are defecting from the evolutionist camp. It is interesting, moreover, that most of these `experts' have abandoned Darwinism, not on the basis of religious faith or biblical persuasions, but strictly on scientific grounds, and in some instances, regretfully, as one could say."
J. Wolfgang Smith, Ph.D. Mathematics, MS Physics, 'Telhardism and the New Religion" 1988, Tan Books and Publishers Inc..


ON BIOLOGY:


"The fact of evolution is the backbone of biology, And biology is thus in the peculiar position of being a science founded on an unproved theory - is it then a science or a faith ? Belief in the theory of evolution is thus exactly parallel to a belief in special creation - both are concepts which believers know to be true but neither, up to the present, has been capable of proof." Evolutionist L. Harrison
Matthews, FRS, Introduction to Darwins "The Origin of the Species", J.M. Dent &
Sons LTD, London, 1971, p xi.


ON ABIOGENESIS (Evolution of life from non-living matter)


"More than 30 years of experimentation on the origin of life in the fields of chemical and molecular evolution have led to a better perception of the immensity of the problem of the origin of life on Earth rather than to it's solution. At present all discussions on principal theories and experiments in the field either end in a stalemate or in a confession of ignorance."


"Considerable disgreement between scientists have arisen about detailed evolutionary steps. The problem is that principal evolutionary processes from prebiotic , molecules to progenotes have not been proven by experimentation and the processes by which these proceeses occurred are not known. Moreover, we do not actually know where the genetic information of all livings cells originates, how the first replicable polynucleotides (nucleic acids) evolved, or how the extremely complex structure-function relationships in modern cells came into existence."

"It appears the field has now reach a stalemate, a stage in which hypothetical arguments dominate over facts on based on experimentation or observation"

[and]

"In spite of many attempts, there have been no breakthrough during the past 30 years to help the origin of chiralty in living cells,"
Klaus Dose, Interdisciplinary Science Reviews, 1988, 13(4) 348.


Eminent Evolutionist, A.I. Oparin, In the preface of Dean Kenyon's book, 'Biochemical Predestination', (Mcgraw Hill, 1969 edition, and was the best selling advanced level book on chemical evolution in the 1970's, written in Professor Kenyon's (Ph.D. Biophysics, BS Physics) evolutionist days) wrote:

"It is not only my professional opinion, but that of many leading evolutionary scientists at present, and in the past as well, that Creation Science and Evolution are the sole scientific alternative explanations, though each have a variety of approaches. ... To sum it up, biological creation is scientific, and in fact is stronger than biological evolution." German Edition (1974).


"My one and only piece of relevant evidence [for an Aristotelian God] is the apparent impossibility of providing a naturalistic theory of the origin from DNA of the first reproducing species ... [In fact] the only reason which I have for beginning to think of believing in a First Cause god is the impossibility of providing a naturalistic account of the origin of the first reproducing organisms." (private interview with Antony Flew, Dec 2004)


On Darwinian evolution:

"The fact that a theory so vague, so insufficiently verifiable,and so far from the criteria of HARD science has become dogma can only be explained on sociological grounds." Biologist Ludwig von Bertalanffy, as quoted by Huston Smith, 'The Post Modern Mind' (New York, Crossroads, 1982) p. 173

On the General Theory of Evolution (Macro-evolution - That all species share a common ancestry)

Professor J. Wolfgang Smith wrote:
"The salient fact is this: If by evolution we mean macroevolution (as we henceforth shall) then it can be said with utmost vigor that the doctrine is totally bereft of scientific sanction. Now, to be sure, given the multitude of extravagant claims about evolution promulgated by evolutionists with an air of scientific infallibility, this may indeed sound strange. And yet the fact remains that there is not a shred of bona fide scientific evidence in support of the thesis that macro evolutionary transformations have ever occurred."

"... We are told dogmatically that evolution is an established fact; but we are never told who has established it, and by what means. We are told, often enough, that the doctrine is founded upon evidence and that indeed this evidence 'is henceforward above all verification, as well as being immune from any subsequent contradiction by experience'; but we are left entirely in the dark on the crucial question wherein, precisely, this evidence consist." Professor J. Wolfgang Smith, Ph.D Mathematics, MS Physics, 'Teilhardism and the New Religion', 1988, Tan Books and Publishers. pp. 2,5,6.


On the interpretation of Scientific Data in support of evolution


"Evolution became in a sense a scientific religion; almost all scientists have accepted it and many are prepared to 'bend' their observations to fit in with it." (Physics Bulletin, "A Physicist
Looks at evolution," Lipson, 1980, Vol. 31,p. 138.)


"Any reasonably graded series of forms can be thought to have legitimacy. In fact, there is circularity in the approach that first assumes some sort of evolutionary relatedness and then assembles a pattern of relationships from which to argue that relatedness must be true. This interplay of data and interpretation is the achilles heel of the second meaning of evolution [Macro-evolution]". Thomson
`Marginalia, the Meaning of Evolution' 70 Am. Scientist 529-530,
(1982).

ON Evolutionists and the Evidence they offer in support of evolution

" I probably will be chastised by them [his more cynical evolutionists colleagues] for writing this preface, as if in doing so I give aid and comfort to an enemy of true science. ... I do so because the book has virtue as criticism of evolutionary theory.


"It has virtue even though its criticism is loaded like the proverbial pair of dice. ... He [creationist W. R. Bird] rolls the dice with style. He rolls them over and over again with the same result. I may be too optimistic to expect my colleagues learn much if anything from Mr. Bird's effort. But there is something in his book for all of them...


"Mr. Bird is concerned with origins and the evidence relevant thereto. He is basically correct that the evidence, or proof, of origins- of the Universe, of life, of all major groups of life, of all the minor groups of life, indeed of all of the species- is weak or nonexistent when measured on an absolute scale, as it always was and will always be.


"He is correct also that what evidence there is, is sometimes, even often, exaggerated by evolutionists. Yes, they load their own dice, for they too, are human. They, too, play to the gallery, to the jury, to the judges. Were they entirely wise rather than adversarial, they would never have claimed to do the impossible: to have proved the correctness of their views by offering evidence of the origin of things. One might just as well attempt to prove stability by offering as evidence a pyramid balanced on its apex." Evolutionist, Gareth J. Nelson, Chairman and Curator, Department of Herpetology and Ichthyology, The American Museum of Natural History, New York, NY, 10024. Preface to W.R, Bird's book, 'The Origin of Species Revisited'.


Evolution as anti-Science:

HL Lipson writes in his published paper 'A Physicist Looks at Evolution' (31 Physics Bulletin 38, 1980) rejects macro evolution. He says:
"I have always been slightly suspicious of the theory of evolution because of it's ability to account for any property of living beings (the long neck of the giraffe, for example). I have therefore tried to see whether biological discoveries over the last thirty years or so fit in with Darwins theory. I do not think they do. ...To my mind, the theory does not stand up at all."

Lipson, an agnostic physicist, goes on to show that the scientific discoveries not only failed to support macro-evolution, but that, at the same time, the evidence also supports creation theory. He concludes:
"I think, however, that we must go further than this and admit that the only acceptable explanation is creation. I know that this is anathema to physicists, as indeed it is to me, but we must not reject a theory that we do not like if the experimental evidence supports it."

In his November 5, 1981 address at the American Museum of Natural History, Evolutionist Dr. Colin Patterson, Curator of the British Museum of Natural History stated at the AMNH address the following with regard to macro-evolution:

"I feel that the effect of hypotheses of common ancestry in systematics has not been merely boring, not just a lack of knowledge; I think it has been positively anti-knowledge... Well, What about evolution? Well we are back to the question I have been putting to people, "Is there one thing you can tell me about evolution?" The absence of answers seem to indicate that it is true, evolution does not convey any knowledge..."

Dr. Guiseppe Sermonti, Professor of Genetics at the University of Peruvia, former director of the Genetics Institute of the University of Palermo, Senior Editor of the Biology Forum, and co-author and paleontologist Dr. R. Fondi (Dopo Darwin, 1980) (Nature, 1982) stated that:


"The result we believe must be striven for can therefore only be the following: Biology will receive no advantage from following the teachings of Lamarck, Darwin, and the modern hyper-Darwinists; Indeed, it must as quickly as possible leave the narrow straits and blind alleys of the evolutionistic myths and resume its certain journey along the open and illuminated paths of tradition."


Muggeridge, Malcolm, The End of Christendom (Grand Rapids: Eerdmans,
1980), p. 59
"I myself am convinced that the theory of evolution, especially the extent to which it's been applied, will be one of the great jokes in the history books in the future. Posterity will marvel that so very flimsy and dubious an hypothesis could be accepted with the incredible credulity that it has."

P. 62
"I think that I spoke to you before about this age as one of the most credulous in history, and I would include evolution as an example. I'm very happy to say I live near a place called Piltdown. I like to drive there because it gives me a special glow. You probably know that a skull was discovered there, and no less than five hundred doctoral theses were written on the subject, and then it was discovered that the skull was a practical joke by a worthy dentist in Hastings who'd hurriedly put a few bones together, not even of the same animal, and buried them and stirred up all this business. So I'm not a great man for bones."

[Chimp]

An example of natural selection....one aspect of the mechanism of evolution.

The peppered moth.

An example of a mutation that has allowed an organism to increase it's population
relative to it's former (unmutated) population: XDR - tuberculosis.

Score one for the blind watch maker!

[Wyvern]

Just a few things about your very old paste job. Abiogenesis is not a part of the ToE. Darwin was only the originator of this theory and the modern version of it has little to do with the original idea. The only people that separate evolution into macro and micro versions are those opposed to the idea in the first place. ID is not science since it only works by invoking a deus ex machina(god, aliens or whatever).

Simply put no matter how much you may dislike it evolution is the best explanation we have right now for how living things change over time. Humans are curious by nature and giving an unsatifactory answer merely sparks more questioning not less even if you invoke divine punishment for doing so.

[twobitsmedia]

Just a few things about your very old paste job. Abiogenesis is not a part of the ToE. Darwin was only the originator of this theory and the modern version of it has little to do with the original idea. The only people that separate evolution into macro and micro versions are those opposed to the idea in the first place. ID is not science since it only works by invoking a deus ex machina(god, aliens or whatever).

Simply put no matter how much you may dislike it evolution is the best explanation we have right now for how living things change over time. Humans are curious by nature and giving an unsatifactory answer merely sparks more questioning not less even if you invoke divine punishment for doing so.

Yes, who needs the right explanation? Lets just stick with the best one.

[Confused]

Just a few things about your very old paste job. Abiogenesis is not a part of the ToE. Darwin was only the originator of this theory and the modern version of it has little to do with the original idea. The only people that separate evolution into macro and micro versions are those opposed to the idea in the first place. ID is not science since it only works by invoking a deus ex machina(god, aliens or whatever).

Simply put no matter how much you may dislike it evolution is the best explanation we have right now for how living things change over time. Humans are curious by nature and giving an unsatifactory answer merely sparks more questioning not less even if you invoke divine punishment for doing so.

Yes, who needs the right explanation? Lets just stick with the best one.

How about we stick with the scientific one since the evaluation is based on the scientific realm?

[Undertow]

Just a few things about your very old paste job. Abiogenesis is not a part of the ToE. Darwin was only the originator of this theory and the modern version of it has little to do with the original idea. The only people that separate evolution into macro and micro versions are those opposed to the idea in the first place. ID is not science since it only works by invoking a deus ex machina(god, aliens or whatever).

Simply put no matter how much you may dislike it evolution is the best explanation we have right now for how living things change over time. Humans are curious by nature and giving an unsatifactory answer merely sparks more questioning not less even if you invoke divine punishment for doing so.

Yes, who needs the right explanation? Lets just stick with the best one.

History shows us that the most data encompassing and pasimonious explanations are more often correct than others. Besides you neglect the point that science dosen't produce absolute truths or certainties.

[Undertow]

My challenge to those who responded is to provide a strong bit of specific scientific evidence that has clearly lead you to accept evolution as being a scientific fact, as so many of you wantonly proclaim. Please be specific and provide one piece of evidence from science at a time. Be prepared to defend whatever convincing scientific evidence you set forth.

You can take this one at a time if you like, the following lead me to conclude that evolution is supported by the genome data (forget what's fact or any such claims of certainty. Evolution is subject to change just like any other theory):

Evidence


Human Chromosome 2:

Human chromosome 2 is the result of the fusion of two ancestral chromosomes in our lineage. This is evidenced by telomere sequence in it's center and two centromeres within the chromosome, one being deactivated. Human chromosome 2 is highly similar in sequence to two chromosomes which remain seperate in the chimpanzee lineage suggesting that we share a common ancestor with chimpanzees and that the fusion event occured after the divergance of our respective linages.

General reading/viewing: [1] [2] [3]

Journal reading:
[1]

Human chromosome 2 was formed by the head-to-head fusion of two ancestral chromosomes that remained separate in other primates.

[2]

The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions.

[3]

We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.

Similarities in chromosome banding patterns and hybridization homologies between ape and human chromosomes suggest that human chromosome 2 arose out of the fusion of two ancestral ape chromosomes (1-3).

[4]

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes.

Endogenous Retroviruses:

Endogenous retroviruses are the genomes of viruses permanently inserted into a population's gene pool due to being inherited through the germ line. When incorporated into a random location along the genome, or locus, the endogenous retrovirus remains and can even be 'copy pasted' to other areas of the genome. When two or more endogenous retroviruses of the same locus between humans and chimps are found, the only reliable explanation to avoid the miniscule chance of them having integrated independantly is inheritance from a common ancestor.

General reading: [1]

Journal reading:
[1]

The human endogenous retrovirus type II (HERVII) family of HERV genomes has been found by Southern blot analysis to be characteristic of humans, apes, and Old World monkeys. New World monkeys and prosimians lack HERVII proviral genomes. Cellular DNAs of humans, common chimpanzees, gorillas, and orangutans, but not lesser ape lar gibbons, appear to contain the HERVII-related HLM-2 proviral genome integrated at the same site (HLM-2 maps to human chromosome 1). This suggests that the ancestral HERVII retrovirus(es) entered the genomes of Old World anthropoids by infection after the divergence of New World monkeys (platyrrhines) but before the evolutionary radiation of large hominoids.

[2]

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.

The genomes of vertebrate species contain dozens to thousands of ERV sequences (2), some of which were acquired in evolutionarily recent times, whereas others derive from "ancient" times, as indicated by their identical site of integration in more than one species (1, 3, 4).

Cross-hybridization and PCR studies consistently reveal that most HERV families are also found in other primates, including apes and Old World monkeys (OWMs) (12-19). Many HERVs, including the ones used in this study, are the result of integration events that took place between 5 and 50 million years ago, as indicated by the distribution of specific proviruses at the same integration sites (or "loci") among related species.

[3]

Like other transposable elements, HERVs are thought to have played an important role in the evolution of mammalian genomes, and the human genome sequence has already been of use in phylogenetic studies of HERVs. By analyzing HERV integration sites, the evolution of these elements has been tracked through the primate lineage. Measurement of the divergence of LTR sequences has also been used as a 'molecular clock' to estimate the age of HERVs (given that the LTRs are identical at the time of integration) [5]. Class I and class III HERVs are the oldest groups and are present throughout the primate lineage, while class II includes HERVs that have been active most recently. Many class II loci are restricted to chimpanzees and humans and a few proviruses of the HERV-K(HLM-2) subgroup are human-specific [6], indicating that these viruses have been active within the last 5 million years.

[4]

We report here that the chimpanzee genome contains at least 42 separate families of endogenous retroviruses, nine of which were not previously identified. All but two (CERV 1/PTERV1 and CERV 2) of the 42 families of chimpanzee endogenous retroviruses were found to have orthologs in humans.

Nine families of chimpanzee endogenous retroviruses have been transpositionally active since chimpanzees and humans diverged from a common ancestor. Seven of these transpositionally active families have orthologs in humans, one of which has also been transpositionally active in humans since the human-chimpanzee divergence about six million years ago.

[5]

Most of the 68 HERV-K14I and 23 HERV-K14CI proviruses are severely mutated, frequently displaying uniform deletions of retroviral genes and long terminal repeats (LTRs). Both HERV families entered the germ line 39 million years ago, as evidenced by homologous sequences in hominoids and Old World primates and calculation of evolutionary ages based on a molecular clock.

The 'Alu' Sequence:

An Alu sequence is a small segment of DNA of around 300 base pairs in length and is repeated millions of times throughout our genome taking up roughly 10% of it's total sequence. Similarly to endogenous retroviruses, the Alu sequence is a transposon (more specifically a retrotransposon) and can 'copy paste' itself, which explains its sheer abundance and distribution around our genome. When two or more Alu sequences of the same locus between humans and chimps are found, the only reliable explanation to avoid the miniscule chance of them having integrated independantly is inheritance from a common ancestor.

General reading: [1]

Journal reading:
[1]

The [alpha globin pseudogenes] genes of both human and chimpanzee are flanked by the same Alu family member. The structure and position of this repeat have not been altered since the divergence of human and chimpanzee, and it is at least as well conserved as its immediate flanking sequence. Comparing human and chimpanzee, the 300 bp Alu repeat has accumulated only two base substitutions and one length mutation; the adjacent 300 bp flanking region has accumulated five base substitutions and twelve length mutations.

[2]

Here we compare the sequences of seven pairs of chimpanzee and human Alu repeats. In each case, with the exception of minor sequence differences, the identical Alu repeat is located at identical sites in the human and chimpanzee genomes. The Alu repeats diverge at the rate expected for nonselected sequences. Sequence conversion has not replaced any of these 14 Alu family members since the divergence between chimpanzee and human.

[3]

Phylogenetic analysis of Alu Ye5 elements and elements from several other subfamilies reveals high levels of support for monophyly of Hominidae, tribe Hominini and subtribe Hominina. Here we present the strongest evidence reported to date for a sister relationship between humans and chimpanzees while clearly distinguishing the chimpanzee and human lineages.

At eight Alu Ye5 loci and two previously identified Alu Yi and Yd loci (18, 45), amplification of filled sites was obtained in human, bonobo, and common chimpanzee.

The utility of SINE insertions, and mobile elements in general, for phylogenetic analysis continues to be bolstered by studies such as this one. Here, we present the first application of SINEs to fully elucidate the phylogeny of the hominid lineage and present the strongest evidence to date for phylogenetic relationships among the hominid lineages. Of the 133 Alu insertion loci, 95 were unambiguously informative for determining the relative divergence of each of the major lineages.

[4]

The Alu Ye lineage appears to have started amplifying relatively early in primate evolution and continued propagating at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes.

For the Ye subfamilies, 120 of the 153 elements identified in the draft human genomic sequence were amplified by PCR. Examination of the orthologous regions of the various species genomes displayed a series of different PCR patterns indicative of the time of retroposition of each of the elements into the primate genomes. Results from a series of these experiments showed a gradient of Ye Alu repeats beginning with some elements that are recent in origin and unique to the human genome (e.g. Ye5AH110) and ending with elements that are found within all ape genomes (e.g. Ye5AH148). The distribution of all the Ye elements in various primate genomes is summarized in Additional File 2. [See the word document file]

[5]

Repetitive elements, particularly SINEs (short interspersed elements) and LINEs (long interspersed elements), provide excellent markers for phylogenetic analysis: their mode of evolution is predominantly homoplasy-free, since they do not typically insert in the same locus of two unrelated lineages, and unidirectional, since they are not precisely excised from a locus with the flanking sequences preserved (Shedlock and Okada 2000 ). Indeed, the use of SINEs and LINEs to elucidate phylogeny has a rich history. SINEs and LINEs have been used to show that hippopotamuses are the closest living relative of whales (Shimamura et al. 1997 ; Nikaido et al. 1999 ), to determine phylogenetic relationships among cichlid fish (Takahashi et al. 2001a ,b ; Terai et al. 2003 ), and to elucidate the phylogeny of eight Primate species, providing the strongest evidence yet that chimps are the closest living relative of humans (Salem et al. 2003 ). In each one of these studies, the presence or absence of a repetitive element at a specific locus in a given species was determined experimentally by PCR analysis, using flanking sequences as primers.

Pseudogenes:

Pseudogenes are defunct genes being either a copy of the original or the original itself. Copies of a gene can arise due to duplication of a genetic segment thus duplicating any genes contained on it where as pseudogenes arising from the original copy arise due to the loss of function of the gene in question. For example, the human olfactory (smell) system is coded for by many genes, 40% of which having become redundant pseudogenes in our linage and prior to. As for endogenous retroviruses and the Alu sequence, when two or more pseudogene sequences of the same locus between humans and chimps are found, the only reliable explanation to avoid the miniscule chance of them having integrated independantly is inheritance from a common ancestor. Also, the same pseudogenes present of defunct copies of functional genes in both humans and chimps allude to common ancestry.

General reading: [1]

Journal reading:
[1]

The olfactory receptor (OR) subgenome harbors the largest known gene family in mammals, disposed in clusters on numerous chromosomes. We have carried out a comparative evolutionary analysis of the best characterized genomic OR gene cluster, on human chromosome 17p13. Fifteen orthologs from chimpanzee (localized to chromosome 19p15), as well as key OR counterparts from other primates, have been identified and sequenced.

We also demonstrate that the functional mammalian OR repertoire has undergone a rapid decline in the past 10 million years: while for the common ancestor of all great apes an intact OR cluster is inferred, in present-day humans and great apes the cluster includes nearly 40% pseudogenes.

[2]

We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates.

Pseudogenes are usually considered the evolutionary endpoint of genomic material whose ultimate fate is to be removed from a genome. Nevertheless, millions of years of evolution has left the human genome with thousands of pseudogenes (Torrents et al. 2003 ; Zhang et al. 2003 ). Within the ENCODE project, the MSA group has identified and sequenced the orthologous regions of the individual ENCODE target regions in 20–28 vertebrate (mostly mammalian) species (see Methods for the list). Several algorithms such as TBA (Threaded Blockset Aligner) (Blanchette et al. 2004 ) have also been applied to construct multispecies sequence alignments across the entire ENCODE regions (The ENCODE Project Consortium 2007 ; Margulies et al. 2007 ). With these data, it is possible to survey the preservation of sequences corresponding to the human pseudogenes in other species to get a glimpse of the evolutionary process leading to the human lineage.

These results demonstrate that most ( 80%) human processed pseudogenes arise from sequences specific to the primate lineage and are in good agreement with previous data estimated with molecular clocks using pseudogenes and SINE (short interspersed elements) repeats (Ohshima et al. 2003 ).

The redundancy of the genetic code:

The genetic code is redundant. This essentially means that different sequences of nucleotides can code for the same protein product. This is due to the fact that there are often multiple codons encoding the release of one amino acid into a polypeptide chain during the cellular process of translation.

Here is a picture of the universal genetic code –



Each three letter sequence, or codon (shown as the RNA version in this case) shows it’s amino acid product. To show an example for the redundancy of the genetic code, take the amino acid Leucine (Leu) as an example. From the universal genetic code, we can see that no less than four codons code for it. This means that the DNA sequences (codons) that code for the amino acid Leucine are GAA, GAG, GAT and GAC (the biologists here will understand why). As a result of this redundancy, it’s not unreasonable to expect that if humans and chimps had arisen independently, that they should have no reason to have any identical genes barring any uncanny and low chance coincidence. Also, any identical genes we do find should go some way to bolstering the inferential evidence for our common ancestry.

General reading: [1]

Journal reading:
[1]

Interestingly, there are several genes that showed the identical nucleotide sequence between different species (see Table 3). For example, both amino acid and nucleotide (coding part) sequences of beta-2 microglobulin were identical among human, chimp, and gorilla genomes, while the interleukin-2 precursor gene sequences from human and gibbon were identical. (Data for other three species were not available.)

[2]

Among the 231 genes associated to a canonical ORF, 179 show a coding sequence of identical length in human and chimpanzee and exhibit similar intron–exon boundaries. For those 179 genes, the average nucleotide and amino acid identity in the coding region is 99.29% and 99.18%, respectively. Of these, 39 genes show an identical amino acid sequence between human and chimpanzee, including seven in which the nucleotide sequence of the coding region is also identical (Supplementary Table 3).

[3]

Here we have sequenced Tau [gene] exons 1-13, including flanking intronic regions, and the region in intron 9 that contains Saitohin in chimpanzees, gorillas, and gibbons. Partial sequences were obtained for cynomolgus macaque and green monkey. Chimpanzee brain tau was 100% identical to human tau. Identities were 99.5% for gorilla tau and 99.0% for gibbon tau. Chimpanzee DNA was polymorphic for a repeat in intron 9, which was present in human and gorilla tau, and for the nucleotide at position +29 of the intron that follows exon 10.

[twobitsmedia]

Just a few things about your very old paste job. Abiogenesis is not a part of the ToE. Darwin was only the originator of this theory and the modern version of it has little to do with the original idea. The only people that separate evolution into macro and micro versions are those opposed to the idea in the first place. ID is not science since it only works by invoking a deus ex machina(god, aliens or whatever).

Simply put no matter how much you may dislike it evolution is the best explanation we have right now for how living things change over time. Humans are curious by nature and giving an unsatifactory answer merely sparks more questioning not less even if you invoke divine punishment for doing so.

Yes, who needs the right explanation? Lets just stick with the best one.

How about we stick with the scientific one since the evaluation is based on the scientific realm?

Scientific realm? What? there is a different realm for science? That explains a lot.
Is it on a map? Does it have anything to do with the philosophical realm or the religious realm, or does it trump it all because it is the "best" explanation?

[twobitsmedia]

Just a few things about your very old paste job. Abiogenesis is not a part of the ToE. Darwin was only the originator of this theory and the modern version of it has little to do with the original idea. The only people that separate evolution into macro and micro versions are those opposed to the idea in the first place. ID is not science since it only works by invoking a deus ex machina(god, aliens or whatever).

Simply put no matter how much you may dislike it evolution is the best explanation we have right now for how living things change over time. Humans are curious by nature and giving an unsatifactory answer merely sparks more questioning not less even if you invoke divine punishment for doing so.

Yes, who needs the right explanation? Lets just stick with the best one.

History shows us that the most data encompassing and pasimonious explanations are more often correct than others. Besides you neglect the point that science dosen't produce absolute truths or certainties.

I havent neglected the point. That IS the point.

[MagusYanam]

Scientific realm? What? there is a different realm for science? That explains a lot.
Is it on a map? Does it have anything to do with the philosophical realm or the religious realm, or does it trump it all because it is the "best" explanation?

Science is the art of the phenomenal. It categorises, measures and explains phenomena in phenomenal terms: that is its sovereign realm. It does not attempt to explain anything in noumenal, metaphysical or aesthetic terms, which is what philosophy and religion attempt to do (among other things). Science cannot 'trump it all' because doing so would be stepping outside its chosen realm.

Life is undeniably a natural, material phenomenon. As such, science is bound by the very foundations of the scientific discipline to ascertain a natural, materialistic cause for life.

What ID does is that it violates the fundamental ground rules for doing science. It tries to give metaphysical explanations for material phenomena.