When the AIDS epidemic hit, people were desperately scrabbling to understand what was going on, because the way in which to begin to try and tackle a problem is to begin to try to understand it.
Laboratories in many parts of the world have contributed to the understanding that we now have, and to the methods we have to cope with it and to combat it.
It turns out that acquired AutoImmune Deficiency Syndrome is caused by a virus, dubbed HIV - Human Immunodeficiency Virus, in which the immune system is fatally compromised.
An enormous amount of effort has been put into studying this virus, especially the way in which it infects us and how it operates. It is an example of a "retrovirus", so named because it goes in the opposite (retro) direction to the then tongue-in-cheek named "central dogma" of biology, in which DNA is transcribed into RNA, and RNA is translated into proteins. With a retrovirus, RNA gets converted to DNA.
Retroviruses have RNA genomes, very similar to, but not exactly the same, as DNA genomes. These RNA genomes include a gene for an enzyme called reverse transcriptase, that, once a target host cell is infected, uses the cell resources to generate a DNA version of its RNA genome. Incidentally, the existence of reverse transcriptase tantalisingly hints at a transition from an "RNA World" to a "DNA World". This enzyme takes RNA and makes DNA. RNA structures assemble naturally, on their own, far more easily than DNA ones ever could.
Now here comes the evil bit. Another retroviral enzyme takes the converted viral genome and does a cut-and-paste, inserting (integrating it, in the jargon) into our own cells' DNA.
When the cells' "machinery" for processing DNA (RNA polymerase) encounters retrovirally derived DNA, it can't tell that it is alien. It just dutifully does its normal thing, creating RNA molecules derived from the DNA which then go on to specify amino acids that then happen to go on to create yet more viral particles to emerge and infect even more host cells.
Fiendish, eh?
So one hope that researchers had was to try to identify how to block integrase from integrating retrovirally derived DNA with our own DNA, and indeed, a class of partially successful drugs called integrase inhibitors has been produced as a result of the intensive study of integrase enzymes. But the research found that the integration site, the DNA locus where integrase cuts and pastes the viral DNA, is not specific. Not precise. It cannot target specific host DNA loci. Yes, there may be regions where integration is more likely to happen, but just as road traffic accidents are more likely to happen in certain stretches of road, each accident is a unique event, never precisely the same as all the others.
Various surveys of integration loci have been made that confirm this lack of targetting specific DNA loci. See https://barryhisblog.blogspot.com/p/relationship-between-integration-sites.html
Now while all this research into HIV was going on, it was known that other retroviruses exist. International consortia of researchers were looking at our DNA and discovering remnants of other retroviruses in our genomes. These are the endogenous retroviruses (ERVs), meaning remnants of retroviral infections that entered our genomes by integrating with the existing DNA of our gametes, and have thereby become heritable. You can inherit them from your parents and pass them down to your offspring exactly as you can inherit and pass on terachromacy, blue eyes, colour blindness, haemophilia and so on.
It turns out that the vast majority of our ERVs are in the exact same DNA locations as one another, comparing the location of each ERV from cell to cell. This is also the case with the cells taken from other members of our species. And because integrase cannot target specific loci, we need an explanation for this. What could explain the same genetics, in exactly the same locations, in all of our cells, in all the members of our species? It couldn't be because of separate infections.
How about inheritance? We all start out as a single cell. A zygote. And as we develop, that cell gets replicated - copied, and all it's DNA gets coped with it, resulting in each of the daughter cell inheriting the exact same DNA as the original zygote.
So commonly located ERVs prove common ancestry. They must all have copies of the viral DNA in the single cell you started out as, and in addition, they must have all been inherited from ancestors we all have in common.
The human genome project https://www.genome.gov/human-genome-project sequenced the human genome and discovered that there are some 200,000 such recognisable ERVs and ERV fragments in our DNA, amounting to about 8% of our DNA.
The chimpanzee's genome was the next one to be sequenced, and it was discovered that the huge majority of ERVs in the chimp's DNA were the same as the human ones and in exactly corresponding DNA loci, down to single base-pair resolution. Remember that integrase cannot precisely target integration sites. The only possible explanation for this finding is that all of these corresponding ERVs descend by inheritance from ancestors that humans and chimps must have shared in common.
This does not disprove God, but it does disprove the idea of separate, special creation. God would surely not have falsified this evidence unnecessarily, just to fool us and lead us astray. The idea strikes one as blasphemous.
If you want to know more, explore my FAQ on this subject which is located @ https://barryhisblog.blogspot.com/p/endogenous-retroviruses-frequently.html
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