All your base are belong to us

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All your base are belong to us

Postby Harvey » Tue May 03, 2022 4:34 pm

https://www.sciencenews.org/article/all-of-the-bases-in-dna-and-rna-have-now-been-found-in-meteorites

All of the bases in DNA and RNA have now been found in meteorites

By Liz Kruesi

April 26, 2022 at 11:00 am

More of the ingredients for life have been found in meteorites.

Space rocks that fell to Earth within the last century contain the five bases that store information in DNA and RNA, scientists report April 26 in Nature Communications.

These “nucleobases” — adenine, guanine, cytosine, thymine and uracil — combine with sugars and phosphates to make up the genetic code of all life on Earth. Whether these basic ingredients for life first came from space or instead formed in a warm soup of earthly chemistry is still not known (SN: 9/24/20). But the discovery adds to evidence that suggests life’s precursors originally came from space, the researchers say.

Scientists have detected bits of adenine, guanine and other organic compounds in meteorites since the 1960s (SN: 8/10/11, SN: 12/4/20). Researchers have also seen hints of uracil, but cytosine and thymine remained elusive, until now.

“We’ve completed the set of all the bases found in DNA and RNA and life on Earth, and they’re present in meteorites,” says astrochemist Daniel Glavin of NASA’s Goddard Space Flight Center in Greenbelt, Md.

A few years ago, geochemist Yasuhiro Oba of Hokkaido University in Sapporo, Japan, and colleagues came up with a technique to gently extract and separate different chemical compounds in liquified meteorite dust and then analyze them.

“Our detection method has orders of magnitude higher sensitivity than that applied in previous studies,” Oba says. Three years ago, the researchers used this same technique to discover ribose, a sugar needed for life, in three meteorites (SN: 11/22/19).

In the new study, Oba and colleagues combined forces with astrochemists at NASA to analyze one of those three meteorite samples and three additional ones, looking for another type of crucial ingredient for life: nucleobases.

The researchers think their milder extraction technique, which uses cold water instead of the usual acid, keeps the compounds intact. “We’re finding this extraction approach is very amenable for these fragile nucleobases,” Glavin says. “It’s more like a cold brew, rather than making hot tea.”

With this technique, Glavin, Oba and their colleagues measured the abundances of the bases and other compounds related to life in four samples from meteorites that fell decades ago in Australia, Kentucky and British Columbia. In all four, the team detected and measured adenine, guanine, cytosine, uracil, thymine, several compounds related to those bases and a few amino acids.

Using the same technique, the team also measured chemical abundances within soil collected from the Australia site and then compared the measured meteorite values with that of the soil. For some detected compounds, the meteorite values were greater than the surrounding soil, which suggests that the compounds came to Earth in these rocks.

But for other detected compounds, including cytosine and uracil, the soil abundances are as much as 20 times as high as in the meteorites. That could point to earthly contamination, says cosmochemist Michael Callahan of Boise State University in Idaho.

“I think [the researchers] positively identified these compounds,” Callahan says. But “they didn’t present enough compelling data to convince me that they’re truly extraterrestrial.” Callahan previously worked at NASA and collaborated with Glavin and others to measure organic materials in meteorites.

But Glavin and his colleagues point to a few specific detected chemicals to support the hypothesis of an interplanetary origin. In the new analysis, the researchers measured more than a dozen other life-related compounds, including isomers of the nucleobases, Glavin says. Isomers have the same chemical formulas as their associated bases, but their ingredients are organized differently. The team found some of those isomers in the meteorites but not in the soil. “If there had been contamination from the soil, we should have seen those isomers in the soil as well. And we didn’t,” he says.

Going directly to the source of such meteorites — pristine asteroids — could clear up the matter. Oba and colleagues are already using their extraction technique on pieces from the surface of the asteroid Ryugu, which Japan’s Hayabusa2 mission brought to Earth in late 2020 (SN: 12/7/20). NASA’s OSIRIS-REx mission is expected to return in September 2023 with similar samples from the asteroid Bennu (SN: 1/15/19).

“We’re really excited about what stories those materials have to tell,” Glavin says.
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Re: All your base are belong to us

Postby DrEvil » Thu Dec 01, 2022 6:29 pm

Here's an article about the research about life possibly being inevitable I mentioned in the "Myth of Progress" thread:

https://www.space.com/37988-did-life-em ... -laws.html

Was the Origin of Life a Fluke? Or Was It Physics?
By Ian O'Neill published August 30, 2017

Understanding the origin of life is arguably one of the most compelling quests for humanity. This quest has inevitably moved beyond the puzzle of life on Earth to whether there's life elsewhere in the universe. Is life on Earth a fluke? Or is life as natural as the universal laws of physics?

Jeremy England, a biophysicist at the Massachusetts Institute of Technology, is trying to answer these profound questions. In 2013, he formulated a hypothesis that physics may spontaneously trigger chemicals to organize themselves in ways that seed "life-like" qualities.

Now, new research by England and a colleague suggests that physics may naturally produce self-replicating chemical reactions, one of the first steps toward creating life from inanimate substances.

This might be interpreted as life originating directly from the fundamental laws of nature, thereby removing luck from the equation. But that would be jumping the gun.

Life had to have come from something; there wasn't always biology. Biology is born from the raw and lifeless chemical components that somehow organized themselves into prebiotic compounds, created the building blocks of life, formed basic microbes and then eventually evolved into the spectacular array of creatures that exist on our planet today. [7 Theories on the Origin of Life]

"Abiogenesis" is when something nonbiological turns into something biological and England thinks thermodynamics might provide the framework that drives life-like behavior in otherwise lifeless chemicals. However, this research doesn't bridge life-like qualities of a physical system with the biological processes themselves, England said.

"I would not say I have done anything to investigate the 'origin of life' per se," England told Live Science. "I think what's interesting to me is the proof of principle – what are the physical requirements for the emergence of life-like behaviors?"

Self-organization in physical systems

When energy is applied to a system, the laws of physics dictate how that energy dissipates. If an external heat source is applied to that system, it will dissipate and reach thermal equilibrium with its surroundings, like a cooling cup of coffee left on a desk. Entropy, or the amount of disorder in the system, will increase as heat dissipates. But some physical systems may be sufficiently out of equilibrium that they "self-organize" to make best use of an external energy source, triggering interesting self-sustaining chemical reactions that prevent the system from reaching thermodynamic equilibrium and thus maintaining an out-of-equilibrium state, England speculates. (It's as if that cup of coffee spontaneously produces a chemical reaction that sustains a hotspot in the center of the fluid, preventing the coffee from cooling to an equilibrium state.) He calls this situation "dissipation-driven adaptation" and this mechanism is what drives life-like qualities in England’s otherwise lifeless physical system.

A key life-like behavior is self-replication, or (from a biological viewpoint) reproduction. This is the basis for all life: It starts simple, replicates, becomes more complex and replicates again. It just so happens that self-replication is also a very efficient way of dissipating heat and increasing entropy in that system.

In a study published July 18 in the journal Proceedings of the National Academy of Sciences, England and co-author Jordan Horowitz tested their hypothesis. They carried out computer simulations on a closed system (or a system that doesn't exchange heat or matter with its surroundings) containing a "soup" of 25 chemicals. Although their setup is very simple, a similar type of soup may have pooled on the surface of a primordial and lifeless Earth. If, say, these chemicals are concentrated and heated by an external source – a hydrothermal vent, for example – the pool of chemicals would need to dissipate that heat in accordance with the second law of thermodynamics. Heat must dissipate and the entropy of the system will inevitably increase.

Under certain initial conditions, he found that these chemicals may optimize the energy applied to the system by self-organizing and undergoing intense reactions to self-replicate. The chemicals fine-tuned themselves naturally. These reactions generate heat that obeys the second law of thermodynamics; entropy will always increase in the system and the chemicals would self-organize and exhibit the life-like behavior of self-replication.

"Essentially, the system tries a bunch of things on a small scale, and once one of them starts experiencing positive feedback, it does not take that long for it to take over the character of organization in the system," England told Live Science.

This is a very simple model of what goes on in biology: chemical energy is burned in cells that are – by their nature – out of equilibrium, driving the metabolic processes that maintain life. But, as England admits, there's a big difference between finding life-like qualities in a virtual chemical soup and life itself.

Sara Imari Walker, a theoretical physicist and astrobiologist at Arizona State University who was not involved in the current research, agrees.

"There’s a two-way bridge that needs to be crossed to try to bridge biology and physics; one is to understand how you get life-like qualities from simple physical systems and the other is to understand how physics can give rise to life," Imari Walker told Live Science. "You need to do both to really understand what properties are unique to life and what properties are characteristic of things that you consider to be almost alive […] like a prebiotic system."

Emergence of life beyond Earth?

Before we can even begin to answer the big question of whether these simple physical systems may influence the emergence of life elsewhere in the universe, it would be better to understand where these systems exist on Earth first.

"If, when you say 'life,' you mean stuff that is as stunningly impressive as a bacterium or anything else with polymerases and DNA, my work doesn't yet tell us anything about how easy or difficult it is to make something that complex, so I shouldn't speculate about what we'd be likely to find elsewhere than Earth," England said. (Polymerases are proteins that assemble DNA and RNA.)

This research doesn't specifically identify how biology emerges from nonbiological systems, only that in some complex chemical situations, surprising self-organization occurs. These simulations do not consider other life-like qualities – such as adaptation to environment or reaction to stimuli. Also, this thermodynamics test on a closed system does not consider the role of information reproduction in life's origins, said Michael Lässig, a statistical physicist and quantitative biologist at the University of Cologne in Germany.

"[This] work is indeed a fascinating result on non-equilibrium chemical networks but it is still a long way from a physics explanation of the origins of life, which requires the reproduction of information," Lässig, who was not involved in the research, told Live Science.

There’s a critical role for information in living systems, added Imari Walker. Just because there appears to be natural self-organization exhibited by a soup of chemicals, it doesn't necessarily mean living organization.

"I think there's a lot of intermediate stages that we have to get through to go from simple ordering to having a full-on information processing architecture like a living cell, which requires something like memory and hereditary," said Imari Walker. "We can clearly get order in physics and non-equilibrium systems, but that doesn't necessarily make it life."

To say England's work could be the "smoking gun" for the origin of life is premature, and there are many other hypotheses as to how life may have emerged from nothing, experts said. But it is a fascinating insight into how physical systems may self-organize in nature. Now that researchers have a general idea about how this thermodynamic system behaves, it would be a nice next step to identify sufficiently out-of-equilibrium physical systems that naturally occur on Earth, England said.


Edit: Also, there's an old alternative to Drake's Equation I've been trying to find, but can't remember what it's called. I think the guy who came up with it was Russian or Eastern European. The intriguing part of it is that it calculates the lifetime of civilizations and how many arise on any given planet on average. I think the Earth came out to about three or four civilizations in its lifetime (including humans).
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Re: All your base are belong to us

Postby Harvey » Fri Dec 02, 2022 8:31 am

I'm importing these too, there's much which can be addressed. I see a number of implied assumptions and think it is possible to suggest some alternative and complimentary considerations, all of which might be fruitful.


DrEvil » Tue Nov 29, 2022 12:53 am wrote:
this is probably only a fraction of it.


You can say that again. The Eurekalert piece left out the title of the paper - "In vitro neurons learn and exhibit sentience when embodied in a simulated game-world".

I guess "We created a sentient Pong slave! Look at it go!" was too incendiary.

It does mention the free energy principle, but not that the guy who came up with it, Karl J. Friston, is a co-author on the paper. The math is so far beyond me it's not even funny, but the basic idea (which I am probably mangling beyond recognition) is fascinating. It essentially boils down to: systems try to minimize surprise. We model our surroundings and try to predict what will happen, and if our predictions fail we reassess our model or change our surroundings to fit our predictions (in other words, politics are hardwired into reality. Damn it!).

Can't wait to see what happens when a more advanced experiment (maybe with robot arms. Robot arms are cool) fails to predict an outcome and decides to change its surroundings to fit.

Peter Watts has his usual uplifting take on the whole thing:
https://www.rifters.com/crawl/?p=10307


A completely different tangent: I'm pretty (a little) sure that entropy plays a part in the above. Minimizing energy spent is usually beneficial, and having to spend time and energy organizing things to fit our predictions or reorganize our internal models spends energy and goes against entropy.

All life really goes against entropy. It's a high-energy state that will naturally decay into a low-energy state if left alone.

Throw in pan-psychism and the implications are a little unnerving. If the universe is sentient/conscious and we're just tiny parts of it, what else follows that basic layout? Our bodies and the cells inside them. In our case, specifically the type of cells that throw their weight around, gobbling up everything around them to spread, also known as cancer. What does our bodies do about that? Immune system GO! Our immune system wipes out cancers all the time and they never amount to anything. How would that apply on the scale of the universe? What if the universe has an immune system, we just haven't become enough of a nuisance to trigger it yet (spreading to another solar system might do the trick)? What if the reason we haven't found anyone else is because the Great Filter is the universe's immune system kicking in whenever someone gets too European?

Anyway, sorry about the detour. The idea "what if life itself is evil" just popped into my head a couple of weeks ago and has been sloshing around in there since, so I just wanted to lay it out and hopefully have someone explain why it has to be wrong.




DrEvil » Tue Nov 29, 2022 8:19 pm wrote:Yeah, I should have clarified. Not intrinsically evil, that was just my starting point before I came up with all the other nonsense, but bad/evil in the same sense we view cancer or a virus: not good for the host, in this case the universe.

Actually, come to think of it, my starting point wasn't even "what if life is evil", but "what if the pan-psychic universe is evil?" (again, not Satan-evil, just not friendly to us). We tend to assume that if there is some greater being/mind/sentience/consciousness it has to be good and wise and all that stuff. I can't think of a good reason why that should be the default. Why isn't it selfish and indifferent to others and mostly concerned with itself, same as most other life we know of? I know for a fact I'm not going to lose any sleep over a virus or bacteria in my body dying, I might even actively work towards getting rid of it. Why should the universe be any different?

Then again, maybe life is the whole point. I've seen some research looking at whether life is a random accident or an intrinsic emergent property of our universe, and the researchers landed on the latter. Pure speculation of course, since we only have a sample size of one, but intriguing nonetheless. If life is inevitable the place should be teeming with it.
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Re: All your base are belong to us

Postby DrEvil » Fri Dec 02, 2022 3:26 pm

Yeah, just to be clear, I don't actually believe this, I'm just spitballing because it's fun, and you can probably pick so many holes in it it falls apart completely. Just the assumption that the universe has any kind of agency is a huge one. That it's hostile to us, or that we could possibly be any kind of threat to it is also, to put it mildly, dodgy. Then again, to paraphrase an old Rigint comment: the universe is billions of light years across, and every inch of it will kill you dead in an instant.

Could probably cobble together a half-decent short story from it though. Scientist investigating the nature of the universe and how everything is connected with quantum woo (throw in some personal stuff to ground it and give it emotional stakes as a counterpoint to the underlying nihilism), with each short chapter divided by small snippets from the news about the first human probe to reach another solar system, which would be the trigger point for the Great Filter. Ends with the scientist realizing the horrible truth and rushing home to deal with $personal_stuff just as the data from the probe gets scary (the probe communicates via quantum entanglement to get around the timing issue) and the talking heads and experts start getting uneasy, and asteroids in the outer system start heading towards Earth, or the sun starts charging up the mother of all solar flares.

I just watched The Lazarus Project, so I'm in an end of the world kind of mood. :)
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Re: All your base are belong to us

Postby Joe Hillshoist » Fri Dec 02, 2022 9:07 pm

DrEvil » 03 Dec 2022 05:26 wrote:Yeah, just to be clear, I don't actually believe this, I'm just spitballing because it's fun, and you can probably pick so many holes in it it falls apart completely. Just the assumption that the universe has any kind of agency is a huge one. That it's hostile to us, or that we could possibly be any kind of threat to it is also, to put it mildly, dodgy. Then again, to paraphrase an old Rigint comment: the universe is billions of light years across, and every inch of it will kill you dead in an instant.

Could probably cobble together a half-decent short story from it though. Scientist investigating the nature of the universe and how everything is connected with quantum woo (throw in some personal stuff to ground it and give it emotional stakes as a counterpoint to the underlying nihilism), with each short chapter divided by small snippets from the news about the first human probe to reach another solar system, which would be the trigger point for the Great Filter. Ends with the scientist realizing the horrible truth and rushing home to deal with $personal_stuff just as the data from the probe gets scary (the probe communicates via quantum entanglement to get around the timing issue) and the talking heads and experts start getting uneasy, and asteroids in the outer system start heading towards Earth, or the sun starts charging up the mother of all solar flares.

I just watched The Lazarus Project, so I'm in an end of the world kind of mood. :)


This is basically the plot of Mass Effect.

The Reapers are the Great Filter. The activation of the space station known as the Citadel, and the use of the mass relay network signals the Reapers to begin their harvest of synthetic and organic stuff of interest to them.
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Re: All your base are belong to us

Postby Harvey » Sat Dec 03, 2022 7:47 am

I'll introduce a few things to chew on - otherwise very busy today.


For Joe, it seems others got there before Mass Effect: http://www.alloya.com/texts/Archonic%20 ... 0dream.pdf


For the discussion, Mircea Sanduloviciu is doing some interesting work on self perpetuating/self organising plasma phenomenon:

On the Physical Basis of Self-Organization: https://www.researchgate.net/scientific ... u-34872884

Physical Basis of Biophoton Emission and Intercellular Communication: http://www.rrp.infim.ro/2008_60_3/43-885-898.pdf

And at the more speculative end of things, Jay Alfred marries all these ideas together.

A Compilation of Essays on Dark Plasma Theory : http://www.ignaciodarnaude.com/ufologia/Alfred,Jay,Dark 20plasma 20theory.pdf
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Re: All your base are belong to us

Postby DrEvil » Wed Dec 07, 2022 11:56 pm

Joe Hillshoist » Sat Dec 03, 2022 3:07 am wrote:
DrEvil » 03 Dec 2022 05:26 wrote:Yeah, just to be clear, I don't actually believe this, I'm just spitballing because it's fun, and you can probably pick so many holes in it it falls apart completely. Just the assumption that the universe has any kind of agency is a huge one. That it's hostile to us, or that we could possibly be any kind of threat to it is also, to put it mildly, dodgy. Then again, to paraphrase an old Rigint comment: the universe is billions of light years across, and every inch of it will kill you dead in an instant.

Could probably cobble together a half-decent short story from it though. Scientist investigating the nature of the universe and how everything is connected with quantum woo (throw in some personal stuff to ground it and give it emotional stakes as a counterpoint to the underlying nihilism), with each short chapter divided by small snippets from the news about the first human probe to reach another solar system, which would be the trigger point for the Great Filter. Ends with the scientist realizing the horrible truth and rushing home to deal with $personal_stuff just as the data from the probe gets scary (the probe communicates via quantum entanglement to get around the timing issue) and the talking heads and experts start getting uneasy, and asteroids in the outer system start heading towards Earth, or the sun starts charging up the mother of all solar flares.

I just watched The Lazarus Project, so I'm in an end of the world kind of mood. :)


This is basically the plot of Mass Effect.

The Reapers are the Great Filter. The activation of the space station known as the Citadel, and the use of the mass relay network signals the Reapers to begin their harvest of synthetic and organic stuff of interest to them.


Can't believe I didn't see this before now. I've only played through the Mass Effect trilogy three times. Now that I see it there's tons of stuff with the same basic premise: Fred Saberhagen's Berserker stories, Alastair Reynold's Revelation Space books, Linda Nagata's Nanotech Succession series, etc.

But to be fair to myself (*pats back*), I was thinking of it as a feature of the universe, not some messed up life-form that evolved inside it. In my version Reapers and friends would all have been wiped out the moment they started spreading. The universe itself would just reach down and snuff them out.

And there would be no god damn color coded ghost in the machine to make everything right! Yes, I'm still sore about the ending to Mass Effect.

And thanks Harvey. Will have to do a deep dive.
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Re: All your base are belong to us

Postby DrEvil » Mon Dec 19, 2022 7:43 am

https://scitechdaily.com/new-theory-sug ... s-likely/#

New Theory Suggests That the Origin of Life on Earth-Like Planets Is Likely

According to a recent paper by a math professor at the University of Arkansas, the existence of life on Earth provides proof that abiogenesis is relatively easy on planets similar to Earth, refuting the “Carter argument” conclusion.

Does the presence of life on Earth provide any insight into the likelihood that abiogenesis—the process by which life first emerges from inorganic substances—occurs elsewhere? That is a question that has baffled scientists for a while, as well as everyone else inclined to think about it.

Astrophysicist Brandon Carter makes the widely accepted claim that the selection effect of our own existence limits our ability to observe. Nothing can be concluded about the likelihood of life existing elsewhere based on the fact that we had to end up on a planet where abiogenesis took place.

He claimed that understanding life on this earth had, at best, neutral value. Another way to look at it is to say that because Earth wasn’t chosen at random from the group of all Earth-like planets, it can’t be seen as a typical Earth-like planet.

However, a recent paper by retired astrophysicist and University of Arkansas mathematics instructor Daniel Whitmire argues that Carter’s logic was flawed. Whitmire contends that Carter’s theory suffers from “The Old Evidence Problem” in Bayesian Confirmation Theory, which is used to update a theory or hypothesis in light of new evidence, despite the fact that it has gained widespread acceptance.

After giving a few examples of how this formula is employed to calculate probabilities and what role old evidence plays, Whitmire turns to what he calls the conception analogy.

As he explains, “One could argue, like Carter, that I exist regardless of whether my conception was hard or easy, and so nothing can be inferred about whether my conception was hard or easy from my existence alone.”

In this analogy, “hard” means contraception was used. “Easy” means no contraception was used. In each case, Whitmire assigns values to these propositions.

Whitmire continues, “However, my existence is old evidence and must be treated as such. When this is done the conclusion is that it is much more probable that my conception was easy. In the abiogenesis case of interest, it’s the same thing. The existence of life on Earth is old evidence and just like in the conception analogy the probability that abiogenesis is easy is much more probable.”

In other words, the evidence of life on Earth is not of neutral value in making the case for life on similar planets. As such, our life suggests that life is more likely to emerge on other Earth-like planets — maybe even on the recent “super-Earth” type planet, LP 890-9b, discovered 100 light years away.

Reference: “Abiogenesis: the Carter argument reconsidered” by Daniel P. Whitmire, 23 September 2022, International Journal of Astrobiology.
DOI: 10.1017/S1473550422000350
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Re: All your base are belong to us

Postby Harvey » Mon Mar 06, 2023 9:59 pm

https://www.cambridge.org/core/journals ... 7A7772C5E5

Abstract

Conventionally, intelligence is seen as a property of individuals. However, it is also known to be a property of collectives. Here, we broaden the idea of intelligence as a collective property and extend it to the planetary scale. We consider the ways in which the appearance of techno-logical intelligence may represent a kind of planetary scale transition, and thus might be seen not as something which happenson a planet butto aplanet, much as some models propose the origin of life itself was a planetary phenomenon. Our approach follows the recognition among researchers that the correct scale to understand key aspects of life and its evolution is planet-ary, as opposed to the more traditional focus on individual species. We explore ways in which the concept may prove useful for three distinct domains: Earth Systems and Exoplanet studies; Anthropocene and Sustainability studies; and the study of Technosignatures and the Search for Extraterrestrial Intelligence (SETI).
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