That extra genetic code isn't ancient alien viruses. It's part of a message from our forebearers, which has to be combined with genetic code from other alien races in this quadrant.
Given DNA is quantised into just four nucleotides -- and I suspect that there is no organism that uses, say, just three -- then wouldn't your statement be trivially true? That is, pick a 1mer of a random nucleotide (A, C, G or T) and there you go.
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.
Yes, that's sort of what I'm getting at with that leading question. If we accept evolutionary biology then a headline like this wouldn't be all that surprising. All living things converge at the root.
> 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.
What this article is saying, though, is stronger: It's not just convergence to the root, but also branch merges. While those branches will converge to the same root, they may have diverged significantly (such that today, we recognise them as from totally separate organisms).
Yes, generally speaking, but there are genes that were evolved on branches after they separated from ours.
We don't produce chlorophyll even though we share some DNA with plants.
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.
There's an unbroken chain between everything current living thing and the first living thing...
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.
I do believe there's an abstract principle that we share with anything that sustained its structure. Not a specific thing like a set of genes but the underlying set of chaos-avoiding rules that makes living forms living forms.
The RNA world hypothesis proposes that self-replicating RNA molecules proliferated before DNA, which would be that simpler system as it doesn't require complex protein machinery.
The truth of that statement is presently unknown. All that's known for sure is that all life we've found so far shares a common ancestry. It's possible there were multiple abiogenic sources of life and the one we see now just out-competed everything else. So maybe the first living thing has no ancestors alive today.
What's the argument that life couldn't have arisen multiple times? If the conditions for spontaneous generation existed on the primordial Earth, why wouldn't they have held in more than one place and why couldn't genesis have occurred more than once?
Refer to the Singularity & Big Bang some 13 billion years ago, when we and everything in the (known) universe were all crunched together for just the smallest possible length of time....
Here's a thought. Perhaps viruses are picking up DNA from host organisms and transmitting them to new hosts as they pass from one to the next. Viruses that transmit advantageous DNA will survive in our genome. Viral DNA can be particularly useful when it has an impact on the morphological development of an organism, i.e. as it is developing from an embryo. If this is true it is not surprising that we find a lot of activation of retro viruses during embryonic development.
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.
> activation of retro viruses during embryonic development.
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.
"The early embryo is a hotbed of activity for endogenous retroviruses, recent studies have shown. To understand why embryonic cells make viral proteins, scientists have run experiments to see what happens when viral genes are silenced.
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.
We have a LOT of "appropriated" viral code in our own DNA:
"Reverse-transcribed RNA molecules compose a significant portion of the human genome. Many of these RNA molecules were retrovirus genomes either infecting germline cells or having done so in a previous generation but retaining transcriptional activity. This mechanism itself accounts for a quarter of the genomic sequence information of mammals for which there is data."[1]
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.
You are probably right. You know far more than I, but I do have a knack for seeing paradigm shifts coming. Take that as you will, I can't prove it, it's just personal experience. Just try to remember, if this all unravels in favor of my position, that you talked to some guy on the internet who saw it coming. It's getting pretty annoying having called it ahead of time, and no one remembering or caring that I said anything.
The endogenous retrovirus story is getting quite interesting, particularly in dementia. Some of the top genes associated with brain atrophy appear to be genes important for suppressing retroviral activity. See FUS and TDP43.
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.
37 comments
[ 3.2 ms ] story [ 99.5 ms ] threadThere was a ST:TNG episode about this.
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.
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 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.
Very interesting novel and unlike a lot of comments on the web I found it a really engaging read.
Why keep spamming nytimes?
https://news.ycombinator.com/item?id=15416932
Or maybe we already infected AI