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In Test Tubes, RNA Molecules Evolve into a Tiny Ecosystem (quantamagazine.org)
117 points by nsoonhui on May 6, 2022 | hide | past | favorite | 36 comments


> “By round 190, the researchers had hit on a new surprise: The huge dynamic swings in the population of each lineage had started giving way to smaller waves. This stabilization suggested that the lineages were no longer competing to replicate. Instead, they had started to interact as a network and cooperate in a state of quasi-stable coexistence.”

A very interesting experiment. I know this is reaching, but I wonder what round human being would be on right now if we were in a “test tube” of sorts.


It is a less reaching idea than you first suggest: https://en.m.wikipedia.org/wiki/Simulation_hypothesis


Maybe those UAP's are just the species that started the experiment checking in on it's progress.


Why would they not make themselves undetectable when doing so? Also, if they were actually actually simulators, they would presumably be able to observe everything in the simulation in arbitrary detail without disturbing it or injecting themselves into it.


Unless their stimulus is an intended part of the experiment.


I read thinking it is was just RNA molecules in the test tubes, but they added ribosomes (protein-based enzyme translation machinery) to the mix.

You could think of ribosomes and other cellular proteins as the system hardware and DNA/RNA the software.

Whilst this experiment is nonetheless interesting, even more so the 'RNA world' theory of how life evolved from just RNA molecules, functioning as both enzymes (ribozymes) and genetic material - code that _is_ the hardware, and built itself!


I was explaining the mRNA vaccines to my dad who has... a tough time getting them, and the analogy I used was that ribosomes are like tiny 3D printers which print whatever is encoded in mRNA. Normally these are proteins and structures for your own body whose specs are copied over from DNA, but when the mRNA vaccine enters the cell the ribosomes 3D-print a single COVID spike, which then triggers an immune response.


That's a nice explanation.

If I were him I'd ask why not just print the spikes at the vaccine factory and inject them?

TBH I'm not sure if it's easier/cheaper to use the 3D-printers in our cells, or its more about accurate delivery to the right places, or something else.


Some educated guesses:

1. We don't have "ribosomes at scale"

2. We don't have a way to separate the ribosome product from the factory

3. Keeping the product stable is hard


Another interesting reason is that if you do it the mRNA way, you will continue to internally produce those spike proteins to train your immune system for a week or two


Basically it takes longer to produce them at scale, and they've been less effective at preventing covid infection in clinical trials.


The non-mRNA vaccines do work like that. They use big vats of bacteria as bioreactors and ship the finished product.

Long term, mRNA is a more flexible solution - just ship the blueprints and let people make it themselves.


What stops new spike proteins from being printed endlessly and damaging the immune system?

The newly released Pfizer documents show that some people experienced severe reactions to the vaccine, up to and including death. Many of the severe reactions mirrored reactions to COVID itself. Isn't the spike protein itself the dangerous part of the virus?


> Isn't the spike protein itself the dangerous part of the virus?

No. The dangerous part is the genetic payload of the virus, which hijacks your cells, forcing them to make more of copies of the virus.

Spike protein is just a part of the viral machinery. But it is the part your immune system reacts to.


> What stops new spike proteins from being printed endlessly and damaging the immune system?

The RNA breaks down quickly and predictably and then it stops being picked up by the ribosomes.

> damaging the immune system

The immune system exists to look at, catalogue, and react to things like foreign proteins. The spike protein get made and ejected from your cells into interstitial fluids. From there they flow into lymph nodes. Special cells in the lymph nodes make anti-bodies and record the shape of the protein in anticipation of seeing it again in the future. Think of that as the second line of defense, with the anti-bodies being the first line. Anti-bodies prevent infection, and the cells that recognize the protein on the virus fight and infection if it happens.

> The newly released Pfizer documents show that some people experienced severe reactions to the vaccine

This is the immune response. The adaptive immune system can over react to stimuli for lack of a better work and trigger cascades of neutrophils and other immune cells and proteins to flood you circulatory system. The main weapon of these immune responses is inflammation which is stressful on your body. But pathogens, vaccines, or any number of things could trigger this response.


> The RNA breaks down quickly and predictably and then it stops being picked up by the ribosomes.

That was the story the officials told skeptics in the beginning. We now know it's much longer: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8786601/

"In contrast to disrupted germinal centers (GCs) in lymph nodes during infection, mRNA vaccination stimulates robust GCs containing vaccine mRNA and spike antigen up to 8 weeks postvaccination in some cases"

> The spike protein get made and ejected from your cells

The spike protein is actually slightly modified to anchor itself to your cells, not to be ejected by them. Which begs the question -- what's the implications of expressing an antigen on the surface of your own genetic material? Are auto-immune diseases a risk?

> and the cells that recognize the protein on the virus fight and infection if it happens.

The covid vaccines produce a version of the spike protein which hasn't been seen in 2 years. Additionally, they don't produce any proteins found on other portions of the virus. This results in a rather ineffective vaccine with incredibly narrow immunity. At this point - it's obvious producing a long gone spike protein does not result in an effective covid vaccine.

> This is the immune response.

You don't know this. The lipid nanoparticles are shown to travel to every corner of the body within hours of the injection. It does not stay in the muscle (as we were initially told). What are the implications of your entire body producing spike protein? Are the nanolipids toxic? Turns out the mRNA vaccine finds its way into breastmilk and is causing hepatitis in children. Quit acting like you're a source of authority.

You are a source of misinformation. Covid vaccines failed because people like you decided to trust the science. Try challenging voices of authority next time.


Billions of vaccines administered and no reports of statistically significant complications, let alone deaths as a result. Please stop spreading FUD


Getting a blood clot is a significant complication that does result in death sometimes.

FDA puts strict limits on Johnson & Johnson Covid-19 vaccine

https://www.cnn.com/2022/05/05/health/fda-johnson-johnson-va...


The discussion here is mostly about the mRNA vaccines, and the J&J vaccine uses a viral vector like more traditional vaccines.

EDIT: For what it's worth I think you original question was fine to ask. There's a lot to know about here if you don't want to trust experts and take what they say at face value.


What do you make of the data that from Ontario. https://covid-19.ontario.ca/data?fbclid=1

The vaccinated are getting infected at same or higher rates. (3rd graph)

Walgreens also shows the vaccinated testing positive now at much higher rates too (3rd page):

https://www.walgreens.com/businesssolutions/covid-19-index.j...

And if you look at the ICU numbers of Ontario, the indicator most touted as being proof the vaccine saves lives. The ratio of the ICU patients of the vaccinated/unvaccinated has been growing significantly.

If there is an advantage to being vaccinated. The numbers of the ICU unvaccinated patients are so small, 30 unvaccinated ICU cases per 15 million (Ontario Population) it would really be error prone to extrapolate to the general population from them. For example, it could easily be that 30 people out of a population 15 million are terminally ill with weeks to live, can't or won't take the vaccine then catch covid while being in the Hospital. This has no bearing on how a normal healthy person from the general population would react to COVID.

Ontario doesn't release data on death rates, so we don't know if the unvaccinated die at the same rate once in ICU. They probably don't.

If there is an advantage to being vaccinated at preventing death in absolute terms, it's tiny. The risk of dying from COVID is very small at this point to begin with.


My guess without have to do a bunch of reading and number crunching is that vaccinated people weren’t getting earlier variants but now when faced with a variation that the vaccine is poorly matched to, they’re getting sick but less so than someone who is COVID naive. However the unvaccinated in many cases have had COVID a few times. Many of these people were hospitalized in the past. Among that population there is a lot of natural immunity built up from infections from other variants, which may provide better protection against the latest covid than vaccines. But that’s all a wild ass guess.

[edit] I really don’t get why people are so animated by some cautious speculation, that’s presented as just that but don’t have anything to say in reply.


And even then, the J&J complications are so rare that no feasible amount of clinical testing would have ever uncovered them.

The FDA is right to pull the plug on it, because safer and better vaccines are widely available. But that should not be taken to mean that the J&J vaccine poses any considerable risk to patients, especially compared to those posed by exposure to COVID without a vaccine.


Deadly blood clots are also a significant complication of not getting vaccinated.


Most people that come in contact with COVID don't get infected. Whereas everyone that takes the vaccine will get the spike protein.


> Most people that come in contact with COVID don't get infected.

This is flat out false. Some 2/3 of Americans have already been infected. Go back to the Fox News comments sections.


> Most people that come in contact with COVID don't get infected.

Yes.

> Whereas everyone that takes the vaccine will get the spike protein.

Erm, yes? That's the point. That's what the vaccine is for.


Please stop. Covid vaccines did not fail and are incredibly safe. They have saved millions of lives. The source of misinformation is you.


Interestingly this account is 1 hour old. I would love to know how this works. Is that person paid? Or is he on a personal disinformation mission? Does he believe in the seemingly carefully crafted lies he writes?


Probably just someone who is really animated about the topic, and hasn't grappled with the underlying biology very much. There's a lot to take in and understand about how the immune system works, I don't fault people for misunderstanding it or even having strong distrust for pharma. I try to respond with that in mind, and assume people aren't being malevolent. Even if they are, it's useful to publicly shoot down bad ideas and bullshit.


> That was the story the officials told skeptics in the beginning. We now know it's much longer:

The paper you linker is about lymph serology and antibodies, not the persistence of mRNA in cell. RNAs in general have a median half life of just 2.4 minutes, just chemically. THat's basic science and super well established.

> The spike protein is actually slightly modified to anchor itself to your cells, not to be ejected by them.

The basic mechanism is that the spike proteins make it to lymph nodes, they need to leave the cell to do that. The proteins leave the cell by exocytosis, basic cell transport. The spike binds to ACE2 receptors, and there aren't necessarily many of those on skeletal muscle cells. Sot he spikes float around in the interstitial fluid until it gets flushed through the lymph system and into lymph nodes, where immunity is built.

> Which begs the question -- what's the implications of expressing an antigen on the surface of your own genetic material? Are auto-immune diseases a risk?

Your genetic material is inside of the nucleus of your cells. Auto-immune diseases aren't a risk, the spikes aren't part of your cells.

> The covid vaccines produce a version of the spike protein which hasn't been seen in 2 years

It's similar enough that your immune system will recognize it, even if the antibodies aren't specific enough. B cells and T cells will still see spike covered sheaths of viruses as unfriendly after vaccination. That's why vaccines reduce hospitalization, even when they may not prevent infection for a particular variant. If the spike changed enough to be unrecognizable, it probably wouldn't bind to ACE2 receptors anymore.

> Additionally, they don't produce any proteins found on other portions of the virus. This results in a rather ineffective vaccine with incredibly narrow immunity

That as I explained isn't how immunity works, it's multilayered. The antibodies may no longer be specific enough, but the adaptive immune system still has plenty to work with.

> You don't know this. The lipid nanoparticles are shown to travel to every corner of the body within hours of the injection

We basically do. All of the parts of the vaccine will travel through the lymph system over the course of a day or so, that's how the lymph system works, and that's how all vaccines work. Lipid nano particles are just little tiny globules of fats, they get filtered out by the lymph nodes and spleen and then excreted in solid waste.

> Turns out the mRNA vaccine finds its way into breastmilk and is causing hepatitis in children

There have been 7 documented cases of auto-immune hepatitis after mRNA vaccines and non through breast milk. All vaccines carry risks of dangerous auto-immune responses for a small set of individuals and always have.

> Quit acting like you're a source of authority.

I just like reading books and bio-science papers, and got really into immune system science a few years ago because I have asthma and allergies. The papers aren't hard to read after you nail down basic terminology.

> You are a source of misinformation.

I don't know what this means in context. I'm basically quoting from a cell biology textbook for a lot of this stuff.

> Covid vaccines failed

They've been pretty effective in disconnecting infection from hospitalization, which I don't think is a controversial position.

> because people like you decided to trust the science.

I don't know what "the science" is. I'm not taking any of this on religious faith. There's a lot of published research at this point, and the underlying biology isn't THAT hard to understand at a basic level.


At a little bigger scale, animal cells collect into tiny multicellular "xenobots" in test tubes that run around and collect other cells. https://www.youtube.com/watch?v=-Bwq1oOST7w


The emergence of host-parasite coevolution parallels what happened among the programs that inhabited the original Tierra artificial life experiment: http://tomray.me/pubs/alife2/Ray1991AnApproachToTheSynthesis...


Does this give more support for the theory that all life on Earth started from a few strands of RNA that hitched rides on some asteroids? I wonder what would happen after thousands, or millions of rounds of their experiment?


That’s a question of protein synthesis. This experiment included E. coli material so it leapt over that assumedly-long phase.


Adding asteroids to that hypothesis only makes it (far) less likely; and also raises more questions (how did that RNA arise; and why didn't it happen on Earth?)


That and the Alien movies




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