There follow three sections to choose from, a simple explanation, an executive summary, and a fuller explanation with links to more information, including links to the peer-reviewed scientific literature.
● This looks hard. Do you have a simple explanation?
From The Time Machine 1960, directed by George Pal, based on the 1895 novel by H.G. Wells.
Adapted from Wikipedia: "By the year AD 802,701, humanity has evolved into two separate species: the Eloi and the Morlocks. The Eloi live a life of ease on the surface, while the Morlocks live underground, tending machinery and providing for the Eloi. Having nothing they need to do, the Eloi have slowly become like cattle, smaller than modern humans with sub-human intelligence. All they do is feed, play, and mate. When one of them, Weena, falls into a river, none of the other Eloi help her. She is rescued instead by the Time Traveler. Every so often the Morlocks capture individual Eloi for food, and because this typically happens on moonless nights, the Eloi are terrified of darkness."
How would we prove that the Eloi and the Morlocks had indeed both descended from modern humans? Well, we have signatures in our DNA that were written by retroviruses.
They put their DNA into the DNA of our cells to "fool" them into making new retroviruses.
Sometimes, a retrovirus puts its DNA into the DNA of an egg or sperm cell. When this happens, it becomes heritable - you can inherit it from your parents and pass it down to your offspring. These heritable bits of viral DNA are called ERVs - Endogenous RetroViruses. Fortunately, they no longer fully perform their original functions, otherwise, humans would be extinct.
The signature of any endogenous retrovirus is that it can be found in exactly the same place in the DNA of every single one of your nuclear cells (every cell with a nucleus - which is most of them). The viral DNA ends up in the same place because it, along with all the rest of your DNA, is copied from the DNA of the original single cell you started out as. In contrast, the viral DNA that you have acquired from viruses in the environment is not present in all of your nuclear cells, and in those where it is present, the viral DNA ends up in different points in your DNA, comparing one infected cell with another.
To recap: Viral DNA in the same place in the DNA of every cell means that it is inherited.
Viral DNA in different places in only some of your cells means that you have caught a virus from the environment.
Now, if we find that all the Eloi have the same viral DNA as us, in every cell, in exactly the same places as us, we know that they must have inherited it from us, and therefore we are their ancestors.
The same goes for the Morlocks. The same viral DNA in the same places in every cell means that the Morlocks also descend from us.
Note that we do not even need to look at our own DNA! If we find the same viral DNA in the same places in the DNA of every cell of every Eloi and Morlock, they have to have had common ancestors from which they inherited it (us!). Bear this in mind when this book talks about, not Eloi and Morlocks, but humans and chimpanzees!
● Endogenous Retroviruses as Proof of Evolution (An Executive Summary)
There are elements in our DNA that appear to have been inserted into (integrated with) our species' germ-line DNA by retroviruses. For evidence of this, go here. We call these elements endogenous retroviruses or "ERVs".
Retroviruses cannot target specific DNA loci when they integrate with a host's DNA.
This viral DNA, integrated with the DNA of every one of your nuclear cells, at the same point (locus), going from cell to cell, means that they have been inherited from your ancestors, rather than acquired from the environment. Infections from the environment result in integrations in different loci, and they do not appear in every cell.
The vast majority of ERVs in your DNA are also present in the DNA of chimpanzees, in precisely corresponding DNA loci. This means that humans and chimps must have inherited the same ERVs from ancestors common to both species.
Although elements of ERVs are known to perform useful, and even essential functions, no complete ERVs exist in our genomes. A complete working copy of a retrovirus (a provirus) would prevent development from a zygote. Some elements of ERVs appear to do nothing, and others are implicated in genetic diseases. The idea that ERVs were part of the original "design" of our genomes is a non-starter.
There is often talk about the similarities and differences between the genomes of humans and chimpanzees, and how the percentage comparisons can differ depending on the comparison method used. But common ERVs are not mere "similarities". Each common ERV is a copy of a copy of a copy etc. of a single integration of a retrovirus with the DNA of a single individual's gamete. That gamete is ancestral to all humans and chimpanzees.
Although some people who call themselves Christians (or followers of Islam or Judaism) claim that science is incompatible with their faiths, this is by no means universal. Many denominations and organisations accept the reality of evolution. One of the best-known experts in this field happens to be a Christian preacher.
I use the word "proof" in the title even though many people shy away from it in the context of science, saying that proof belongs to axiomatics and the measuring the alcohol content of beverages, but it has been used in the legal sense, of "proof beyond reasonable doubt". There are no reasonable doubts about what these ERVs tell us.
● What is the "case for common descent" from ERVs?
There follows a summary. Much more detail can be found @ Evolutionary Model
Further FAQ entries go into the following points in more depth and answer common questions about them.
Retroviruses replicate by invading the cells of host organisms, converting their RNA genomes into DNA, and inserting (integrating, in the jargon) the DNA into the DNA of the host cell. The integrated DNA is called a "provirus". The host cell then "reads" the provirus, converting it back into RNA, resulting in the production of more viruses.
Retroviruses tend to target certain types of cells. Their "envelope" proteins tend to be specialized to attach to the surfaces of these cells.
The integration into the host's DNA is made by a retroviral enzyme called integrase. While certain retroviruses can show a general tendency to integrate their DNA in certain types of regions in a host cell's DNA, they do not target specific points (loci). This means that in an infected individual, not all cells will be infected, and in those that are, the retroviral integration will be in a different locus or loci in the DNA of each cell.
We find, in the genomes of creatures such as ourselves and chimpanzees, inherited structures that cannot be anything but the remnants of retroviral integrations. Some are more complete than others, but many have the full set of genes that would be necessary for a complete retrovirus, were they not faulty. We call these structures endogenous retroviruses (ERVs). Unlike the case where each cell is individually infected, they appear in the exact same loci in the DNA of every single nuclear cell (cells with nuclei containing DNA).
Although certain components of some ERVs perform functions in the host, some even being essential in many cases, no complete ERVs are functional. Design, as an explanation for ERVs, does not make any sense. A designer would have no need to include specifically retroviral genes in its designs, which now do nothing, or may even cause harm. There would also be no need to design in non-functional traces of the action of integrase, traces of which are present in ERVs.
The only explanation that makes any sense is that ERVs are the result of retroviral integrations with germ-line DNA - the DNA of egg cells or sperm cells, followed by reproduction and consequent cell division. Cell division will duplicate the ERVs in the same loci in the DNA of every cell. Separate, parallel infection would not infect every cell, and the proviruses would end up in different loci, comparing one infected cell with another.
All human beings have some 200,000+ ERV and ERV fragments in the DNA of every one of their cells. Most of them are in identical DNA loci going from cell to cell, and person to person. This means that we all share common ancestors - the ancestors that first acquired each of the germ-line retroviral integrations.
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