Darwin did not know about DNA and genetics, or how genes were passed down from generation to generation and selected for. To have our evolution be so driven by viruses embedded in our DNA would have sounded crazy to him. These viruses, in particular retroviruses, have provided yet another tool to investigate ancestral relationships between animals, besides the homologous structures Darwin studied. In fact, Darwin would have expected that organisms that were infected by these viruses would be selected against in nature, as they were less fit, and so died early, meaning they had a lesser chance to reproduce.
I thought that the concept of viruses, specifically retroviruses, playing a beneficial role in an organism’s life was surprising. Reading that retroviruses made it possible for mammals to develop placentas and therefore develop a direct line of nutrition from mother to offspring, and therefore allowing the offspring to develop larger brains was a surprise for me. The idea of the genetic material of harmful viruses incorporating itself into an organism’s genome seems fantastical, even paradoxical. However paradoxical, the remains of these retroviruses make up 8% of our DNA. This incorporation eliminates the threat of retroviruses in organisms, a very different process from an organism’s regular defense, in which harmful molecules are broken down or inhibited. However, this allows the immunity to retroviruses to be passed down to successive generations.
The article suggests that the pieces of retroviruses found in the DNA of an organism play a significant role in its evolution. An example of this is the development of the placenta, as I mentioned before. Although retroviruses may seem to pose a health risk to the mother and offspring, it was found that mechanisms in the retroviruses actually mirrored those of proteins found in placental cells, which allowed them to fuse together to form a placenta. This information caused me to change my opinions and understanding of viruses. When, before, I viewed them as simply harmful, I now see that retroviruses play a significant role in our own evolution. The study of retroviruses is even indicating some potential treatments to viral diseases like HIV that we can possibly eradicate it in the future.
While I definitely did not think so before reading the article, I see now that there is an advantage to reviving dead viruses for scientific purposes. If scientists can use their records of extinct viruses to recreate and observe them, they can gain new perspectives on how to eliminate them. While resurrecting dead things sounds like something from a science fiction movie, the knowledge gained would prove invaluable to future organisms’ survival. Studying these retroviruses would allow scientists to pinpoint the processes that caused many of them to become extinct, so that we replicate the process.
Evolving Organisms 
It is fascinating to think about how much slower evolution may have taken place without viruses. Perhaps viruses are one of the most important factors in determining how and when one species branched off from another throughout the evolutionary processes. It is also interesting that some viruses in our DNA have been allowing us protection against other viruses. In order for viruses to incorporate their genetic information into ours, some of our human ancestors must have somehow resisted harm by those viruses. This article made me wonder how this was possible, and how aggressively the viruses affected those who were not equipped to survive in their presence.
By recreating dead viruses, it may be possible for this process to occur again, but it would come with a cost. I completely agree that this kind of research could result in life changing knowledge, but there would certainly be a lot of controversy over it. Scientists would have to observe how various organisms respond to different viruses (whether previously extinct or not), and the consequences of these studies could be severe—we simply we do not know what the results would look like. However, some people would argue that this is exactly why we must conduct research on how extinct viruses would affect modern organisms. There is also the question of what specifically caused those viruses to become extinct. It is possible that organisms had adapted to the viruses and evolved some kind of protection against them. If that is true, then it may even more difficult to take advantage of research involving the reconstruction of dead viruses.
When scientists deal with the reality of reproducing presently-extinct viruses, we, not only as a society, but also as an entire species, have to answer a billion-dollar question: is this a good thing? On the seemingly-positive side, recreating already-extinct viruses gives scientists the potential to help prevent the infection of current diseases within the human population; vaccines can be created from the knowledge garnered from the genomes of the extinct endogenous retroviruses, which would help to stop any further disease-spreading in a population. But what many people do not take into consideration is that implementing vaccines is not always a positive thing — we, as a people, give scientists the go-ahead to play God and heavily influence, and even dictate, the way our species develops and evolves; scientists mess with natural selection and play it out the way that they want it to go, the way that we all give a blind-eye to, mostly because we never stop to think about the potentially negative effects of a thing that looks so nice and shiny on the outside. As Luis P. Villarreal predicted, “without an effective AIDS vaccine, nearly the entire population of Africa will eventually perish. ‘We can also expect at least a few hundred humans to survive,’ he wrote. They would be people who have been infected with H.I.V. yet, for some reason, do not get sick. ‘These survivors would thus be left to repopulate the continent. However, the resulting human population would be distinct’ from those whom H.I.V. makes sick. … The process might take tens, or even hundreds, of thousands of years, but Darwinian selection would ultimately favor such mutations, and provide the opportunity for the evolution of a fitter human population. ‘If this were to be the outcome … we would see a new species of human, marked by its newly acquired endogenous viruses.’”. If left untampered with, viruses could create a whole new, fitter, more adapted species. We have to analyze both the short-term and the long-term benefits before we can come to a valid conclusion about whether or not we should use our knowledge of viruses to change the course of human evolution. The short-term benefit of this type of tampering would be the saving of hundreds of thousands of lives worldwide from a myriad of diseases; the long-term cost would be the loss of a new and better species of human in the future. Before a can proceed in the world of genomic engineering, we have to ask ourselves some very important questions: who are we to take control over the natural order of things? who are we to play God? who are we to vie with Mother Nature?
I also, before reading this article, did not think that viruses could be advantageous to organisms. Yet, after reading this article it makes complete sense that a virus could cause some extreme natural selection to occur. Furthermore, I found that the remains of old retroviruses takes up about almost ten percent of our DNA, to be very surprising. Ten percent is a very large number, considering how important DNA is! It was interesting to learn about Pan troglodytes, which is the virus seen in some primates but not humans that makes us vulnerable to H.I.V. But, this also frustrated me; in the article, they stated that the reason we do not have PtERV in our DNA is that
“we developed a way to repel the virus.” I was frustrated because they said the reason why we developed a way to repel the virus and primates did not was because “we have a defense against this thing that they don’t have…” which wound up being TRIM5a- a protein that destroys PtERV. But this only leads me to believe that we probably developed TRIM5a from a virus, and that there is a never ending cycle of speciation by viruses!
I found reading about the new ways being researched to eradicate the HIV virus to be very intriguing. It fascinated me the unique methods scientists were using to try and pinpoint what process makes viruses extinct. The one method I found the most impressive was Koronis Pharmaceutical’s method, which was actually speeding the life cycle of the AIDS virus to drive it to extinction. The article explained this method earlier stating “The faster a cell reproduces, the more errors it is likely to make. And the more errors it makes the less likely it is to be dangerous to the host.” I found it delightful that instead of trying to slow and stop a virus, it could possibly be more advantageous to speed up the virus until it is going so fast it makes too many errors and basically self-destructs.
I completely agree with the way the article changed your mind about viruses. I felt the same way. In class we were reminded several times that mutations are not necessarily “good” or “bad” – although from an evolutionary standpoint it increases diversity – but I did not really make the connection that it could be the same for viruses as well. To think that the placenta is the result of embryos acting almost like parasites and attaching to the lining of a womb, it blew my mind a little. I thought that was one of the most interesting examples used in Specter’s article. Ever since I had learned that mammals like the platypus laid eggs, I always thought that they were strange, that they were an exception and branched off much earlier along the phylogenic tree. However, in actuality it was us who branched off first. Like you said, this article completely changed the way I thought about viruses. Some of them have had an enormous effect on making humans how we are today.
I had the same thoughts as you Maria! I was very surprised when I read the passage on placentas. It is a strange revelation to come to when you realize that the thing that you were taught to despise and recognize as a threat was actually something that shaped who you are. Given the general public’s current view on viruses, it is strange to see science suddenly turn around and discover that viruses have given us so many benefits. This sort of served as a lesson for us all, to always keep one’s mind open. Because scientists were always focused on the potential harm a virus could cause, the benefits were overlooked. Seeing viruses as key players in the evolution of humans gives us a whole new perspective. With new opportunities to observe viral evolution at play in koalas, I am extremely curious as to how the koalas will adapt.
I agree with your post in its entirety. We had similar interpretations of viruses after reading the article and found the same things to be surprising. I too found it shocking that almost a tenth of our DNA contains remains of retroviruses. This implies that there are potential benefits to retroviruses, and that they should not be seen in a negative light. Studying extinct retroviruses to their full extent would be pertinent in understanding how they have come to evolve so aggressively, and in good hands, may allow scientists to eliminate ones that continue to exist and cause harm to the improvement of society (ex: HIV).