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Endogenous Retroviruses and human evolution.

Discussion in 'Science and Technology' started by shunyadragon, Jul 3, 2017.

  1. shunyadragon

    shunyadragon shunyadragon
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    Endogenous Retroviruses
    This thread will address questions from creationists and those that simply wants to know more about evolution about the case for common descent from endogenous retroviruses (ERVs).

    This may be above the bar for many, but I will start With the basics of genetic relationships and the result of the genetic relationships.
     
    #1 shunyadragon, Jul 3, 2017
    Last edited: Jul 3, 2017
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  2. shawn001

    shawn001 Well-Known Member

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  3. omega2xx

    omega2xx Well-Known Member

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    Why don't you start by explaining how the offspring can get a characteristic not in the gene pool of it parents.
     
  4. shunyadragon

    shunyadragon shunyadragon
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    Endogenous Retroviruses are more complex viruses with a primitive nucleus.

    The genetic relationship of life increases as evolution progresses. For Chimpanzees and bonobo's we share 99% of DNA, for retroviruses all species share ~5% in key location on genome of the DNA that support common descent.

    From: https://www.researchgate.net/publication/227607673_Endogenous_Retroviruses_and_Human_Evolution
    "Abstract

    Humans share about 99% of their genomic DNA with chimpanzees and bonobos; thus, the differences between these species are unlikely to be in gene content but could be caused by inherited changes in regulatory systems. Endogenous retroviruses (ERVs) comprise ∼ 5% of the human genome. The LTRs of ERVs contain many regulatory sequences, such as promoters, enhancers, polyadenylation signals and factor-binding sites. Thus, they can influence the expression of nearby human genes. All known human-specific LTRs belong to the HERV-K (human ERV) family, the most active family in the human genome. It is likely that some of these ERVs could have integrated into regulatory regions of the human genome, and therefore could have had an impact on the expression of adjacent genes, which have consequently contributed to human evolution. This review discusses possible functional consequences of ERV integration in active coding regions."

    Endogenous Retroviruses and Human Evolution (PDF Download Available). Available from: https://www.researchgate.net/publication/227607673_Endogenous_Retroviruses_and_Human_Evolution [accessed Jul 4, 2017].

    From:ERVs
    "Introduction

    A powerful source of evidence that modern species diverged from ancestral species via descent with modification is that of endogenous retroviruses (ERVs). ERV evidence consists of three independent layers that corroborate one another. As will be further discussed, the three layers of ERV evidence are: 1) the sharing of ERVs in identical loci among organisms of varying degrees of taxonomic separation, and the nested hierarchies that these shared ERVs are arranged in; 2) the examination of shared mutagenic discrepancies between shared ERVs, so as to infer relative sequence of insertion; and 3) the nested hierarchies of shared mutations among given ERVs in identical loci. But before this evidence can be examined, one must have a firm understanding of retroviruses and how they infect cells.



    Targeting HIV replication, n.d.). Once integrated, and in DNA form, its genome is known as a prototype retrovirus, or provirus. Upon integration, the cell is allowed to divide, and eventually the presence of certain environmental conditions trigger proviral activation. Copy after copy of the retrovirus is produced as virions bud off, mature, and go on to infect other cells, leading to the death of the infected cell.

    [​IMG]
    The would-be problem for the retrovirus is that once the cell replicates and activation occurs, the provirus relies on the RNA polymerase II of the host cell to transcribe it into viral RNA to be packed into its virions. Unfortunately, RNA polymerase II is designed to transcribe messenger RNA (mRNA) for translation into polypeptides, so although it uses promoters to initiate transcription, since they don’t code for amino acids, it doesn’t transcribe them. With only one set of promoters on the proviruses, the newly transcribed retroviral genomes would have no promoters at all. When the virions that contained them would reverse transcribe and insert them into new host cells, the second round of activation and transcription would never be able to occur.
    Retroviruses circumvent the problem of vanishing promoters by simply polymerizing copies of them during reverse transcription. They achieve this by possessing identical sections of DNA, called repeats, on either terminus of their genome. Early in the process of reverse transcription, the first jump occurs, in which the transfer RNA (tRNA) primer detaches and the DNA repeat hybridizes with the remaining RNA repeat at the genome’s 3’ terminus (Cann, n.d.). Given the relatively small size of the repeats, if they are not identical, they cannot hybridize. As for the 5’ unique (U5) and 3’ unique (U3) sections, a copy of each is polymerized on the opposite terminus. Between the necessity of identical repeats, and the duplication of unique sections, the resulting U3-R-U5 sections, called long terminal repeats (LTRs), must likewise be identical at the time of insertion. This will become very important later on in examining the second and third layers of ERV evidence.
    "
     
  5. shunyadragon

    shunyadragon shunyadragon
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    This has been described a number of times in past threads. Very simply a genetic mutation and change in the offspring of the next generation. This has been observed many times in genetic mutations in recent history,

    This is not the topic of the thread, which is the support of the science of evolution by comparative genetics between Endogenous Retroviruses and humans. Actually in this discussion will address some of the mechanism of related mutations in DNA of later generations related to this relationship will be addressed.
     
  6. shunyadragon

    shunyadragon shunyadragon
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    Actually, this research demonstrates this, answers your question, and described in the following.

    From: ERVs

    Three Layers of Endogenous Retroviral Evidence for the Evolutionary Model

    "The targets of retroviruses are usually somatic cells, but if the infected cell happens to be a sperm or egg cell, known as a gamete, or a testicular or ovarian cell that divides into a gamete, that gamete may be used to produce an offspring. In such a case, the provirus becomes a permanent fixture within the offspring’s genome. Its permanence is due to fact that “there is no mechanism for removing proviruses precisely from the genome, without leaving behind a solo LTR or deleting chromosomal DNA (Johnson and Coffin, 1999).” Although the retrovirus was foreign to the organism it infected, and thus would be considered exogenous to that organism, once passed on to the organisms offspring, it would be present in the offspring’s natural, healthy state, and thus would considered endogenous to it.

    Now being passed on from one generation to the next, ERVs accumulate copying mistakes by DNA polymerase during subsequent host cell replication. Since ERVs are generally not conserved, they accumulate mutations at the same rate as introns. And, as with introns, over time, the mutations can become fixed in the host population’s gene pool (Boeke and Stoye, 1997. In Coffin, Hughes, & Varmus, 1997). Given enough time, enough mutations accumulate to render the ERV incapable of activation.

    If two or more individuals have ERVs of the same family at the same loci, one might think that there exist two plausible explanations: 1) that a retrovirus inserted in a common ancestor, and was passed on to the individuals via sexual reproduction; or 2) that separate retroviruses inserted in the same loci in separate ancestors, and were passed on to the individuals from each respective ancestor. What rules out the latter of these explanations for the majority of shared ERVs is the highly random nature of integration discussed earlier, and shared mutation among ERVs in identical loci, to be discussed shortly.

    Thus, we can then conclude—regardless of how many individuals have retroviruses in the same loci of their genomes—the majority of those retrovirus necessarily inserted within the genomes individual cells of individual ancestral organisms common to each of them, and were passed on to those individuals via sexual reproduction. If the organisms are of the same species the individual from which the insertion originated may likely have also been of the same species. If, however, the organisms are of different species, the shared ERVs are referred to as orthologous, and that is when things get interesting."
     
  7. omega2xx

    omega2xx Well-Known Member

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  8. shunyadragon

    shunyadragon shunyadragon
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    I have had three courses in Genetics. I have a good solid background in genetics, and biochemistry that is why I can discuss this topic. What is your background that you can make these claims which are false?

    No

    Still not the subject of the thread, but nonetheless.
    First, species do not decide to evolve. That is foolish anthroponmorphism.

    Evolution is opportunistic as to available environments, and food sources. The intermediates between the ancestor land animals of whales and whales were coastal species that lived on land and feed in the sea, which had the most abundant food source. There are numerous species living today and found in the fossil record that are coastal mammals that feed in the sea and live on land.
     
  9. omega2xx

    omega2xx Well-Known Member

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    None of what you posted from the expirement indicated it would result in a change of species.
     
  10. shunyadragon

    shunyadragon shunyadragon
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    Check your spelling, and that was not purpose nor topic of the thread.

    What the thread demonstrates that there is an evolving genetic lineage from the
    Endogenous Retroviruses to the human species, and it presents research on how these genetic changes took place in the process of evolution. Not all changes involve simple mutations.

    More to follow . . .
     
    #10 shunyadragon, Jul 4, 2017
    Last edited: Jul 4, 2017
  11. shawn001

    shawn001 Well-Known Member

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    "Try this one---why would a land animal surviving well on land decide to become a whale? That sounds like the opposite of natural selection."

    "
    The First Whale: Pakicetus
    by AMNH on 08/07/2013 12:36 pm

    Odd as it may seem, a four-footed land mammal named Pakicetus, living some 50 million years ago in what we know as Pakistan today, bears the title of “first whale.”

    "Straddling the two worlds of land and sea, the wolf-sized animal was a meat eater that sometimes ate fish, according to chemical evidence. Pakicetus also exhibited characteristics of its anatomy that link it to modern cetaceans, a group made up of whales, porpoises, and dolphins.

    "
    First discovered by paleontologists in 1983, Pakicetus lived along the margins of a large shallow ocean, the Tethys Sea. Although it had the body of a land animal, its head had the distinctive long skull shape of a whale’s.

    Over time, fossils also revealed that Pakicetus had an ear bone with a feature unique to whales and an ankle bone that linked it to artiodactyls, a large order of even-toed hoofed mammals that includes hippos, pigs, sheep, cows, deer, giraffes, antelopes, and even cetaceans, the only aquatic artiodactyls.

    "
    Though rare, mammal species adapting to life in the sea has happened at least seven times in different major groups of mammals.

    Still, this reverse pattern accounts for some 100 living mammal species that inhabit the oceans today, from three major groups."

    The First Whale: Pakicetus

    The environment changed and it was either go back to the sea or starve.


    "The later descendants of Pakicetus were fully aquatic. Modern whales are descended from the archaeocete basilosaurids, a group of toothed whales that had extremely long bodies and tails. The archaeocete basilosaurids appeared later in the Eocene and early Oligocene (34 million to 23 million years ago) and lived in the Tethys Sea and Atlantic Ocean.

    Pakicetus | fossil mammal genus


    Back to viruses.
     
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  12. omega2xx

    omega2xx Well-Known Member

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    Do you never think about and analyze what you are being told? Chemical evidence will not last 50 million years. Eating fish will not cause a change of species. Not only is that absurd, it is not genetically possible. Saying wading in the ocean and eating fish will cause a land animal to become a sea animal , is laughable. You also have on intermediate fossils connecting any land animal to sea life.

    "


    Even if that is true, shape of the head, it still not a mechanism for a change of species. Many unrelated animals have similar characteristics.




    The tympanic bone in whales is unique to whales. It could not have developed from an external ear bone, even with a mutation.


    Talk is cheap and opinions are a dime a dozen. Produce the evidence.

    I guess I am just not that gullible. I need some real scientific evidence to convince me.


    Another opinion for which you offer no evidence. Now think about this. According to evolution, mutations take million of years to change a species. Pakicetus would have become extinct long before it became a whale.




    I think Missouri is looking for a poster for their state motto. Don't submit this, it will not be accepted.



    You finally got something right, but being the same genus does not link pakiceetus to whales


    Maybe you will have better luck there. Make sure you get your shots so you won';t get infected. ;)
     
  13. omega2xx

    omega2xx Well-Known Member

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    Small changes over millions of years does not say HOW it could happen.

     
  14. omega2xx

    omega2xx Well-Known Member

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    Of course genetic changes take place, bu they NEVER result in a change of species. and they are not simple.

    The only changes that take place are determined by the which genes in the parents are passive and which ones are dominant. We know because science has proven which genes are dominant and which ones are passive, although the evidence for that may not be complete yet. In the offspring of a mixed marriage(black and white) the skin color is always dark in varying degrees.
     
  15. shawn001

    shawn001 Well-Known Member

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  16. shunyadragon

    shunyadragon shunyadragon
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    No one ever claimed that is simple.

    Still waiting for you to cite your qualifications concerning your statements concerning the nature of genetics and evolution. Good peer reviewed articles fro journals on Genetics will do, because you apparently have no qualifications in science.
     
  17. shunyadragon

    shunyadragon shunyadragon
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    Excellent layman's presentation on the subject!
     
  18. shunyadragon

    shunyadragon shunyadragon
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    Actually the science of evolution and genetics does explain HOW it happened, but you choose to ignore it based on an archaic Theist agenda. This thread has provided excellent scientific research demonstrates HOW it happened.
     
  19. shunyadragon

    shunyadragon shunyadragon
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    They next discussion will go into the detail of how the DNA can be traced from Retrovirus to human DNA and that of all other species. The methods of tracing our human family ancestors is a simpler process as used to trace the lineage of DNA evolution from Retrovirus to human DNA.

    The reference provided by shawn001 is a good basic reference.

    The Viruses That Made Us Human — NOVA Next | PBS
     
  20. omega2xx

    omega2xx Well-Known Member

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    Still waiting for you to explain, scientifically of course, how mutations are a mechanism for a change of species. All I need is a basic understanding of genetics and mutations, which evidently you are lacking.

    Check what I say with the real scientist at the ICR, who are far better qualified than you are in biology, and tell me why they are wrong.
     
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