This also provides us a clue about how cancer develops. These retro viruses are associated with the changing of form and function of the cell within which they are contained, since they impact this within the development of the embryo. When they are activated within adult cells they drive similar functional changes. Which might be why many cancers, seem, to me, to look like distinct entities, like the tissue has suddenly switched to a different functional mode. It's not just one characteristic of the tissue that has changed to make it dangerous, but a whole constellation of changes that together seem to form a unified whole. I.e. we are looking at groups of changes transported into the genome by a virus that has propagated because those changes are advantageous to the host organism. These changes do not suddenly arise within the body due selection pressures on the tissue, but are activated and mediated by the virus.

This kind of cross species transportation of DNA, could well be analogous to what we see at the microbial level, where horizontal gene transfer is an important driver of evolution.

Citation on this? As far as I know (am writing a phd thesis on development++), there's nothing like "virus activation". Viral elements (mostly transposons) are big evolutionary players but are usually actively repressed by DNA methylation (in eucaryots).

> Which might be why many cancers, seem, to me, to look like distinct entities, like the tissue has suddenly switched to a different functional mode.

I don't 100% understand your comments about viruses here, but related to this, we don't need to imagine some virus orchestrating such a thing (besides, as far as I know they are way too simple to drive complex eucaryot gene regulation), but rather gene regulatory networks which if they get unbalanced can lead to significant changes in morphology.

<edit> some spelling

These experiments suggest that viral proteins help the embryo develop a variety of tissues. "

From the op article.

I'm am not an expert in this at all, these are just my thoughts on the matter, take them or leave them.

Regarding regulatory networks binding together elements so as to orchestrate changes in morphology - I had not thought about this, of course you are correct. Where you say that the viruses are too simple to drive sufficiently complex changes to the regulatory networks, I would counter by saying that chance mutations are sufficient to drive these changes.

But that they are now part of us and when they are activated it's not some virus waking up but parts of viruses that we have adapted into doing useful things for out cells.

Viruses can cause significant changes in gene networks (for example oncoviruses usually suppress tumor-suppressing proteins [2] which dramatically affects things downstream), but the changes are not as holistic as I think you are describing them.

Yes point mutations (and viruses) can derail neural networks and that can have far-reaching consequences, but I think these things are accidental in both cases and not some virus plan as I felt you were arguing.

[1] https://www.sciencedirect.com/science/article/pii/S136952741... [2] https://en.wikipedia.org/wiki/Oncovirus

There was a ST:TNG episode about this.

Very interesting novel and unlike a lot of comments on the web I found it a really engaging read.

There is an increasing body of work in the literature showing that activation of endogenous retroviruses occurs as cells become aged. In many cases, these ancient viral elements in our genome can become activated by external infections.

What I suspect you're getting at is, rather, if our DNA contains virus DNA, then presumably that virus' DNA also contains the DNA of organisms it encountered (using the same mechanism), etc. Thus, there ought to be an unbroken history -- albeit probably highly corrupted from successive adaptive mutations -- in our DNA to the first living thing. This wouldn't necessarily be everything, though; just everything we've assimilated.

That doesn't mean that everything has already been "invented" at the root.

Exactly. The "classical" view of evolutionary genetics is that new genes develop by mutation, are favored (or eliminated) by natural selection, and exchanged only within the same species by interbreeding. So the family tree of life is a map of how closely organisms are related, and they would share a gene only with the nearby branches of the tree descended since that gene arose.

We have long known that the simple model is not complete, prokaryotes (bacteria and archaea) exchange lots of genetic material outside their own "species" (trickier to define for bacteria in any case), but it is becoming more widely recognized that lateral gene exchange happens a lot in all organisms.

A recent popular book on the subject is "The Tangled Tree: A Radical New History of Life" by David Quammen.

Imagine in languages: Indoeuropean languages share a common ancestor, but we can say that suchandsuch word is originally from some language and then adapted into another language and used for potentially different meaning.

I don't think that's an established fact at all. DNA is a very complex system so it's reasonable to think that simpler systems predated it. Not that it affects your reasoning at all, since every current living thing that we know of does use DNA.

Why keep spamming nytimes?

https://news.ycombinator.com/item?id=15416932

Or maybe we already infected AI