pretzellogician
a month ago
Very impressive! To be clear, this is not the smallest known bacterial genome; only the smallest known archaeal bacterial genome, at 238k base pairs.
In the article they mention C. ruddii, with a smaller 159k base pair genome.
But according to wikipedia, it seems N. deltocephalinicola, at 112k base pairs, may be the smallest known bacterial genome. https://en.wikipedia.org/wiki/Nasuia_deltocephalinicola
oersted
a month ago
That’s interesting. The main difference seems to be that those other tiny organisms only encode how to produce some metabolic products for the host but cannot reproduce independently, so they are quite close to being organelles. Instead, this new one pretty much only produces the proteins it needs to reproduce and nothing for the host.
The new one with 238 kbp:
> Sukunaarchaeum encodes the barest minimum of proteins for its own replication, and that’s about all. Most strangely, its genome is missing any hints of the genes required to process and build molecules, outside of those needed to reproduce.
Referencing the 159 kbp one:
> However, these and other super-small bacteria have metabolic genes to produce nutrients, such as amino acids and vitamins, for their hosts. Instead, their genome has cast off much of their ability to reproduce on their own.
flobosg
a month ago
A nitpick: Although similar in some aspects, archaea are not bacteria; they are classified under their own phylogenetic domain.
api
a month ago
[flagged]
smallmancontrov
a month ago
1. Autocatalytic RNA reaction networks -- "soup producing more soup" -- are easily replicated in the lab, subject to Darwinean processes, and are at the center of ongoing study. "0 to Darwin" is now easy, "Darwin to Life" is the new focus, and God of the Gaps must retreat once again.
2. Spores hitchhiking on impact ejecta sounds exotic until you realize that anywhere life is present at all spores will be everywhere and extremely sturdy. That desktop wallpaper you have of planets crashing together and kicking off an epic debris cloud? Everything not molten is full of spores.
3. Religious explanations are not in the same universe of seriousness as 1 and 2. Opening with a religious talking point and closing with a false equivalence is mega sus.
bavell
a month ago
Would love to see some sources for #1. #2 sounds plausible but speculative?
9dev
a month ago
Panspermia is pretty much irrelevant to the actual question though; even assuming life got to Earth the hitchhiker way, it would have to have developed on another planet, and we’re back to square one.
actionfromafar
a month ago
Panspermia is kind of weird to think about IMHO. Because, it likely took a long time to develop and a long time to travel here. So it must have started a long time ago. Before the Solar system was created. But Sol is pretty old. How early could life have started really?
lioeters
a month ago
That gets into astrobiology. Theoretically life could have started as soon as its basic ingredients were ready. So not until things had cooled down a bit after the Bang, when there were heavier elements than hydrogen and helium; and some kind of land and water.
> In the redshift range 100 . (1 + z) . 137, the cosmic microwave background (CMB) had a temperature of 273–373 K (0-100◦C), allowing early rocky planets (if any existed) to have liquid water chemistry on their surface and be habitable, irrespective of their distance from a star.
> In the standard ΛCDM cosmology, the first star-forming halos within our Hubble volume started collapsing at these redshifts,allowing the chemistry of life to possibly begin when the Universe was merely 10–17 million years old.
From: The Habitable Epoch of the Early Universe - https://arxiv.org/abs/1312.0613
In comparison, our beloved sun is estimated to have been born 9.2 billion years after the Big Bang, a third of the way into the universe's history so far.
> The Sun is approximately 4.6 billion years old, while the age of the universe, based on current estimates, is about 13.8 billion years.
So our solar system is not that old, relatively speaking. We're among elders, some stars are three times older than the sun.
> In the future, however, life might continue to emerge on planets orbiting dwarf stars, like our nearest neighbor, Proxima Centauri, which will endure hundreds of times longer than the sun’s.
> Ultimately, it would be desirable for humanity to relocate to a habitable planet around a dwarf star like Proxima Centauri b, where it could keep itself warm near a natural nuclear furnace for up to 10 trillion years into the future.
actionfromafar
a month ago
Wild that the background radiation was a balmy room temperature at one point. Never thought about that.
jiggawatts
a month ago
The earliest galaxies formed when the universe was just a few hundred million years old, which means there may have been planets that are 3x times older than Earth.
Several caveats apply, chiefly that heavy elements weren't produced for a while in significant quantity, but were produced fairly early on due to large stars exploding relatively quickly, when they were merely tens of millions of years old, if that.
smallmancontrov
a month ago
RNA World is really cooking: https://pubmed.ncbi.nlm.nih.gov/39358873/
Ejection: https://link.springer.com/chapter/10.1007/3-540-25736-5_3
Reentry: https://journals.plos.org/plosone/article?id=10.1371/journal...
Not to mention the constant trickle of "X survived in space" stories that we get every time someone bothers to collect and culture a sample. The amount of success at every stage with, frankly, very little effort spent tuning the conditions, multiplied by "bacteria are everywhere" makes hitchhiking less crazy than it sounds. Our intuition misleads us because bacteria are so much better at handling acceleration (easy if you're small) and dessiccation (everywhere is a desert if you're small) than anything we are used to thinking about.
Egret
a month ago
https://pmc.ncbi.nlm.nih.gov/articles/PMC1892545/
An upper bound probability for the RNA world hypothesis is 10^-1018. A reasonable interpretation is that the RNA world hypothesis is impossible in the real world.
avadodin
a month ago
A superficial reading doesn't inspire much confidence in this peer-reviewed article but I agree that RNA-world is a thought experiment at best. There is no evidence of these RNA structures in actual lifeforms. RNA encodes proteins. The most parsimonious explanation is that proteins(likely incapable of true replication by themselves) preceded RNA even if an RNA-based system can be designed in theory. I won't make claims of probability of unknown processes but proteins exist that can assemble spare nucleotides and proteins exist that can assemble proteins out of nucleotide chains. All you need is a pair of them to come in the vicinity of each other and wait until RNA comes along that encodes a similar-enough pair.
Egret
a month ago
The probability of assembling two proteins randomly close by in spatial and temporal terms runs into Chadwick's proximity problem.
user
a month ago
cozyman
a month ago
[flagged]
estimator7292
a month ago
Good news: the primordial oceans were so vast (literally planet-scale) and persisted for so long (millions to billions of years) that you can run a trillion trillion individual random reactions.
You are being severely restricted by your imagination. You seem to have presupposed that random abiogenesis is impossible and reconstructed the facts to support that claim because you can't conceive of the alternative.
Planets are really, really big. Any one chemical reaction is on the scale of molecules. If you let those figures compound for a long time, the number of total reactions gets very, very large. Far larger than you imagine. Many times more.
andrewflnr
a month ago
Still the wrong question. Life didn't start by brute-forcing the combinatorial cliff of RNA. I'm a fan of metabolism-first, or membrane-first. It was almost certainly thermodynamically favored the whole way.
reedlaw
a month ago
The probability space of a 140-nucleotide chain is 10^84. The estimated number of atoms in the universe is 10^80. The hypothesized RNA self-replicator is far simpler than the 238,000 base pair archaeal genome. But how are they formed? Even the most favorable prebiotic lab conditions have only produced short nucleotide chains. Direct chemical synthesis only recently achieved chains over 1700 nucleotides long [1].
1. https://www.chemistryworld.com/news/first-direct-chemical-sy...
oskarkk
a month ago
To go through all 10^84 possible combinations in a billion years, around 10^67 combinations would have to be "tried" per second. So yeah, it doesn't seem feasible to have one and only correct combination of 140 nucleotides spontaneously appear.
But if the "solution" could be composed of a couple of separate smaller parts, that would be stable and linger for a long time, it would be much easier. 40 nucleotides have 10^24 combinations, so only 10^7 tries per second would be needed... over a billion years. And all of the necessary parts would need to be created and then meet in the same place and somehow combine. So, still not easy, but this case doesn't sound so outrageously improbable.
In the end, maybe it is extremely improbable for life to happen, and only one in 10^n suitable planets develops life, and Earth was just very lucky to experience this peculiar phenomenon.
0134340
a month ago
>Still far, far too complex to occur "randomly," which is fascinating
I don't see the word "random" anywhere in the article. By random maybe you mean it's seemingly indeterministic? Regardless of the nature of the underlying process, at the classical level, the environment acts as a deterministic filter, ie, other chemical processes.
alonmower
a month ago
If you’re interested in this area I highly recommend “The Vital Question” by Nick Lane if you haven’t read it.
The TLDR of his theory is that life originated in alkaline hydrothermal vents on the ocean floor, where natural energy gradients could have driven primitive metabolic reactions before the development of DNA.
Book goes into a lot of layperson-accessible detail.
ferfumarma
a month ago
> Still far, far too complex to occur "randomly," which is fascinating
Why spend time making this point? Nobody believes that this occurred randomly: it occurred via evolution.
The mutations are a random part of evolution, but the process overall is not random at all - no more so than your immune system (which randomly generates antibodies, then selects against those that target innate epitopes), or stable diffusion (which starts with random noise, then marches up a gradient toward a known target).
It is the selection step that makes similar processes non-random, because a random selection step would just be noise.
threethirtytwo
a month ago
This is technically random. The entire creationist argument is that complexity cannot come from randomness but evolution is the method in which it does.
Evolution is just a sort of way for low entropy structures to form from randomness. It’s still random all the way down.
The man is just trying to reconcile a belief in god with the scientific reality. He needs to bend the evidence to fit his identity he cannot bend his identity to fit the evidence because that could break his identity. The fact he commented here on this topic is sort of unhinged. It seems like the article presented evidence that is strikingly against his world view and he needed to justify something in order to prevent his identity from rearranging itself according to external reality.
hellofriend_
a month ago
Look, the leap from “a human in a lab coat mixed some chemicals and got something that grows and divides” to “therefore no God (or no transcendent intelligence) is necessary for life to exist”
is not a valid inference. It is a category error dressed up as science.
Demonstrating that intelligence can produce life (or a lifelike system) is the opposite of demonstrating that intelligence is not required. It is literally evidence in favor of the design hypothesis, not against it. The only thing it would rule out is a very narrow version of young-earth creationism that says “God would never let any natural process produce life under any circumstance”.
Also, scaling from “possible on a planet” to “therefore no intelligence was required anywhere in the process” is still the same non sequitur, moving the (apparent) design from the origin of the first cell to the origin of the cosmic initial conditions and laws that permit planetary abiogenesis.
This equation of “intelligent design = creationism = Adam and Eve” is a cultural artifact of the American culture wars, not a reflection of logic or the global scientific community.
threethirtytwo
a month ago
>Look, the leap from “a human in a lab coat mixed some chemicals and got something that grows and divides” to “therefore no God (or no transcendent intelligence) is necessary for life to exist”
That is not my chain of reasoning, nor has lab created life has ever been created. So what you're saying can never be used as valid proof of creationism. And I certainly did not use that evidence to make such a claim. Additionally I never said god does exist or does not exist.
hellofriend_
a month ago
[dead]
akomtu
a month ago
"It's all random all the way down" is just another religious belief. Besides, has anyone estimated the probability of creating organisms so complex using this random evolution scheme? Another problem is why would randomly-evolved organisms be so geometrically symmetric? I'd expect a random process to create an unholy blob of matter.
rcxdude
a month ago
You're lacking imagination and understanding of how these systems form. Symmetry is very commonplace in nature, for very unsurprising reasons, because what's random is how the processes that create those forms change over time, not the entirety of those processes themselves. And yes, there is a huge amount of study of how life could form in the kinds of environments we think existed on earth near the start of life. ATM it's not so much 'how could this happen at all' and more 'what looks like the most likely way that it happened'.
threethirtytwo
a month ago
It's not. It's derived from real time observation, logical induction and other historical evidence that's inline with logic and observation. See my other reply to a sibling commenter of yours.
cozyman
a month ago
[flagged]
fwip
a month ago
"Change kinds" is something that only people who believe in a rather literal view of the Christian bible say, and only because that's the popular fundamentalist argument against evolution.
Fundamentally, it's impossible to reconstruct something from the fossil record that's convincing to these folks, because they will always arbitrarily decide "fossil 1 is kind X, and fossil 2 is kind Y, you need to find me fossil 1.5," no matter how close in time and likeness the fossils are.
So what they actually want is "evolve a lizard species into cats" which fundamentally misrepresents both A) how evolution works (it does not concern itself with human categories) and B) the vast timescale over which small changes accrue.
"Kinds" are just human categories we've mapped onto the results of billions of years of evolution after the fact.
cozyman
a month ago
Is there any way to demonstrate it or is it only an unfalsifiable claim that requires unfathomably long timelines?
rcxdude
a month ago
The entire fossil record and the mountains of shared DNA between very different creatures is pretty compelling evidence. Not to mention the idea of changing 'kinds' is an entirely human-derived categorisation, not something that has some natural definition.
threethirtytwo
a month ago
Easy. Covid evolved forms. The genes are different. There are measurable differences in DNA. These are slight.
So from real time observation we know viruses and bacteria can mutate and have small delta changes in their DNA.
From this we can deduce that over long period of time many small changes can equate to big changes in DNA.
Because we know DNA describes macro characteristics of all living beings and effects behavior, physicality and speciation by logic we know that through induction many many small changes together equals big change and thus evolution can result in speciation and different creatures.
This is the literal conclusion through Direct observation and the inescapable logic of induction. Not to mention it's inline with fossil evidence AND covid is clearly not the only species where we observe mutations. Mutations are observed everywhere, including humans. Cancer is mutation and selection as well.
cozyman
a month ago
This isn't convincing to me, I'm not disputing that mutations exist. Do they become different categories of being?
Macro Evolution has always seemed like a philosophy/ideology/religion to me with a veneer of science.
threethirtytwo
a month ago
Doesn't have to be convincing to you. It's a fact and inescapable conclusion. If you're not convinced, you're wrong.
If mutations can happen, then by logic many mutations can happen, if many mutations can happen then many many mutations can stack up and cause speciation. By believing in mutations, evolution follows via logical induction.
Your DNA can be edited with many many mutations until it becomes indistinguishable from penguin DNA. Take that DNA and insert it into an zygote embryo and you get a penguin, not a human.
This is not a conclusion formed by observation. This is basic logic, 1 + 1 = 2. If the axiom is mutation, evolution is the logical theorem that follows. It is undeniable.
You have to go through a lot of mental gymnastics to deny this logic, but it's worth it if such mental gymnastics formulates a conclusion that remains inline with your religious identity. People without this bias who don't have truth tied to their identity don't need to do this kind of thing.
api
a month ago
People misread my comment as creationism.
The point I was making was that the complexity curve has to meet the floor at some point, and thinking about how this happens and what that looks like is interesting.
I was familiar with RNA world but wasn't aware of how much progress had been made.
andrewflnr
a month ago
Unfortunately your comment is mostly indistinguishable from the kind of "just asking questions" thing actual creationists occasionally post. And you did draw in at least one actual creationist in your replies. Sorry dude. :D Anyway, as a couple of us mentioned, be sure to check out Nick Lane's theories.