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applied science

Composite Creatures

When we look deep into our bodies How much of what we find is Human and how much is . . . something else?

During this COVID-19 crisis a lot of things are posted by many, many people – so much by so many that filtering and actively avoiding too much exposure to this torrent of stuff has become a continuous process for me.

Please don’t get me wrong – I do stay up to date but I do that from reputable news and science sources. Stuff from social media I tend to not pay much attention to. But I do pay some attention and yesterday I was glad that I did.

My friend Richard posted a link to an article on Medium called “Misinformation Goes Viral”. The piece is by Jason Shepherd an Associate Professor of Neurobiology at the University of Utah who specializes in the molecular mechanisms of memory and brain plasticity. He also has his own website (https://shepherdlab.org/) regarding this work:

The Medium article’s main thrust, and my friend’s reason for citing it, was to have a number of the scarier ‘theories’ floating around the internet addressed by someone who knows viruses and human biology. And that part is interesting but . . . the part that got me excited was the two links (1,2) before that part. The ones that he added to show the reader he’s really a working scientist and not some quack flapping his beak.

Those links introduced me to a concept I hadn’t encountered before (I think) that added a whole new chapter to the book of our biology. An essential one that without which we would not exist.

The experience of reading and listening to what his work has revealed was akin to that I felt when I learned that the engines, the Mitochondria, that power every cell in our bodies aren’t human at all.

Mitochondria are Bacteria that colonized an animal cell very far back in the past. That cell and the bacteria were able to coexist in a mutually beneficial arrangement. The cell gave the bacteria a protected environment with nourishment and ‘house cleaning’ while the bacteria provided material the cell could use for power. And it’s been that way ever since. It’s also a reason why we lack the cellular ability to provide our own power – we don’t need to. Almost every cell in our bodies uses them for power. And the same can be said of almost all animals.

Now I find out that it looks like a similar thing happened with our DNA a long time in the past. Possibly more than once.

At some point in the past evolutionary tree we’re part of a cell was invaded by a virus. The invasion by the mitochondria was different matter: an actual fully developed bacteria lives within the cells of our bodies. An invasion by a virus differs from that because a virus has no cell body of its own so the thing it does is to invade the DNA of the target cell inserting its own DNA in the process.

When a disease causing virus does this it turns the cell into a little virus producing factory. The cell begins to spew many new copies of the virus which then go on to attack other cells in the host.

This invasion I’m talking about gave us a gene called ARC. Many animals have an ARC gene but each one is unique to that animal.

When genes are activated they transcribe into RNA molecules which then produce Proteins. In humans the ARC gene only operates in the cells in the brain where it produces a proteins. These proteins are passed from one neuron to another.

In mice bred to not have the ARC gene test show that they cannot lay down long term memories . . . meaning ARC is essential to the process of memory.

These proteins seemed to be far larger than most proteins and they wanted to know why that was. One way to find out was to image them When Sheperd went to look at these proteins he was struck by their appearance – they looked a lot like Viruses. Specifically HIV viruses.

That’s not a coincidence. The team showed that Arc descends from an ancient group of genes called gypsy retrotransposons, which exist in the genomes of various animals, but can behave like their own independent entities.* They can make new copies of themselves, and paste those duplicates elsewhere in their host genomes. At some point, some of these genes gained the ability to enclose themselves in a shell of proteins and leave their host cells entirely. That was the origin of retroviruses—the virus family that includes HIV.
So, Arc genes are the evolutionary cousins of these viruses, which explains why they produce shells that look so similar. Specifically, Arc is closely related to a viral gene called gag, which retroviruses like HIV use to build the protein shells that enclose their genetic material. Other scientists had noticed this similarity before. In 2006, one team searched for human genes that look like gag, and they included Arc in their list of candidates. They never followed up on that hint, and “as neuroscientists, we never looked at the genomic papers so we didn’t find it until much later,” says Shepherd.

https://www.theatlantic.com/science/archive/2018/01/brain-cells-can-share-information-using-a-gene-that-came-from-viruses/550403/

It turns out that ARC can also provide an encapsulating protein shield for the RNA. And the protected RNA package is carried to the target neuron where it alters that neuron’s DNA . . . why and what happens as a result we don’t know yet.

Which brings me around to the reason Shepherd started looking at all this in the first place. If Proteins existence can be measure in hours than how are long term memories formed?

If it were encoded in proteins there would have to be a massive refreshing of proteins on a regular basis like computer DRAM memory requires. That would require a lot of energy expenditure and chemical processing, also meaning possible waste byproducts to be processed. So memory can’t be encoded strictly in proteins. If it’s not proteins then what? Which led to the search and the perplexing partial result of ARC.

So it’s possible that memory is only possible because we were hijacked by a virus a long time ago. And that may not be the only process in our bodies that benefits, or is only possible, courtesy of viruses. Over 100 gag type genes have been found within the human genome . . . we’re just beginning to see that there’s a huge hidden viral iceberg of knowledge within the genome we didn’t even realize was there.

Here’s Jason Shepherd in a TedMed talk.

By xamble

Most things I do involve computers. Nowadays that sounds stupid to hear because everyone uses computers. Except I was saying that before the IBM PC came on the scene. (hint: my first programs were entered on punch cards in an IBM-29)
Now I mostly use them.
Mostly to provide a community service in my small town. Because I could when it was asked and still can.
And I'm a wannabe writer. Various books in various states of incompleteness. A few short stories. Might do more of that.

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