Non-Darwinian Wordle

[Jimmy Higgins]

Were they really?

 

[fromderinside]

The result is widespread evil, in Portland, Seattle, Chicago, and other cesspools driven by Leftists.

Prompts memory of a famous Trump blurb, "Sad".

Neigh and the glue factory.

 

[Swammerdami]

Evolution of life on Earth can be broken into four phases:

1. The development of LUCA from random organic goo developing in the micropores of alkaline thermal vents.
2. The development of a wide variety of bacteria and archaea from LUCA.
3. The development of the first Eukaryote with mitochondria, a complex cell nucleus, and sexual reproduction.
4. The development of plants, animals, fungus etc. from early Eukaryote.

I once read an article from some "science journalist" who wrote something like " ... blah blah and LUCA — the last universal common ancestor of all life — came into being. After that, evolution could begin."

NONSENSE! The evolution just to get to LUCA was huge, and perhaps more impressive than all the rest. The genetic code was already implemented in LUCA with dozens of RNAs and proteins in support and a marvelous ribosome machine. LUCA is also assumed to possess, among other features, an ATP synthase machine similar to (but more primitive than) the one depicted here:

I'm afraid I'll be taking the Pariah's place and branded a Christian or worse. So I'll don my asbestos suit before nailing myself to a cross and admitting that I'm impressed random search could arrive at the marvelous machine which is LUCA.

There are bacteria and fungi that can feed on plastics, even though most plastics are a century old or less, and at most two centuries:  Timeline of plastic development

Some bacteria think plastic is fantastic

Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source

Is it just a coincidence that Ideonella sakaiensis is in the same Class (Betaproteobacteria) as the once-dreaded pathogen Neisseria gonorrhoeae?

 

[Jarhyn]

Evolution of life on Earth can be broken into four phases:

1. The development of LUCA from random organic goo developing in the micropores of alkaline thermal vents.
2. The development of a wide variety of bacteria and archaea from LUCA.
3. The development of the first Eukaryote with mitochondria, a complex cell nucleus, and sexual reproduction.
4. The development of plants, animals, fungus etc. from early Eukaryote.

I once read an article from some "science journalist" who wrote something like " ... blah blah and LUCA — the last universal common ancestor of all life — came into being. After that, evolution could begin."

NONSENSE! The evolution just to get to LUCA was huge, and perhaps more impressive than all the rest. The genetic code was already implemented in LUCA with dozens of RNAs and proteins in support and a marvelous ribosome machine. LUCA is also assumed to possess, among other features, an ATP synthase machine similar to (but more primitive than) the one depicted here:

I'm afraid I'll be taking the Pariah's place and branded a Christian or worse. So I'll don my asbestos suit before nailing myself to a cross and admitting that I'm impressed random search could arrive at the marvelous machine which is LUCA.

Don't get me wrong, but like... That's a really sexy animation. I almost touched myself when I saw it.

Remember, it's not random search, it's just "first thing that worked". It's like lightning sending rivulets of condensed ions that dig towards least action representing a connection of poles until they connect and then the charge travels through the connected ion path's length.

Once anything works, metabolic preference would just... It wouldn't be kind to whatever had existed before.

It's like the evolution of the ability to manufacture JET FUEL in a world that had only known raw wood as fuel.

Do we have any evidence that our current or historic viral population is entirely post-LUCA?

 

[lpetrich]

The LUCA is the most recent common ancestor of every cellular organism. It was a full-scale organism, much like present-day methanogens. It had a full-scale DNA-RNA-protein transcription and translation system and full-scale biosynthesis, making it autotrophic. It got its energy off of chemical reactions of inorganic substrates like hydrogen and carbon dioxide. It did not use oxygen, and it would likely be poisoned by present-day concentrations of oxygen.

It's evident that the LUCA had a lot of evolution behind it -- it's rather difficult to imagine direct prebiotic origin for such an organism.

That is where the RNA world comes it. It is an earlier stage where RNA was both information storage and enzyme. Its continued presence and functions are thus vestigial features. BTW, many vestigial features are functional, and they are identified as vestigial by their structure.

 

[Jarhyn]

The LUCA is the most recent common ancestor of every cellular organism. It was a full-scale organism, much like present-day methanogens. It had a full-scale DNA-RNA-protein transcription and translation system and full-scale biosynthesis, making it autotrophic. It got its energy off of chemical reactions of inorganic substrates like hydrogen and carbon dioxide. It did not use oxygen, and it would likely be poisoned by present-day concentrations of oxygen.

It's evident that the LUCA had a lot of evolution behind it -- it's rather difficult to imagine direct prebiotic origin for such an organism.

That is where the RNA world comes it. It is an earlier stage where RNA was both information storage and enzyme. Its continued presence and functions are thus vestigial features. BTW, many vestigial features are functional, and they are identified as vestigial by their structure.

I would say vestigial would be more descriptive of their preexistence and demotion in the hierarchy of the system's information cycle.

"It is a vestige of it's former glory, such that it is vestigial."

It still technically plays information transport roles.

I like to think A Species of Life is like a Hoarder that collects stuff because it never knows when it's going to be useful again, but is at least fairly good at keeping the clutter from disrupting the operations of the system. DNA was just better positioned as an organic basis to store gobs of junk information, while RNA was better at forming messages. It didn't change from RNA, but a lot of RNA forms just stopped being competitive in the ecosystem.

I find myself wondering when the first selection of a reverse transcriptase happened WRT LUCA.

This is why I am curious about the timeline of viral evolution WRT LUCA... It would suggest events which would strongly favor the precipitation of RNA encodings of proteins to DNA and the large-scale Exodus from the RNA world.

 

[lpetrich]

[*]

I would say vestigial would be more descriptive of their preexistence and demotion in the hierarchy of the system's information cycle.

"It is a vestige of it's former glory, such that it is vestigial."

It still technically plays information transport roles.

Vestigial features are identified as vestigial from being smaller and/or doing less. RNA used to do a lot, but DNA and proteins have taken over most of its former functions.

DNA building blocks are made from RNA ones. The first step is reduction of ribose to deoxyribose, giving uracil DNA or u-DNA. The next step is adding a methyl group to uracil, making thymine.

Proteins are a more complicated story, because ribosomes are RNA-protein complexes. But the key parts of ribosomes are their RNA, and also involved are transfer RNA's, which are connected to protein building blocks. So ribosomes likely originated as ribozymes, with proteins being added later as protein synthesis improved.

 

[lpetrich]

About vestigial features, creationists like to point to anatomist Robert Wiedersheim's 1893 list of 86 human vestigial features, claiming that most of them are now discredited. That list has three types of features:

• Persistent features still considered vestigial
• Transient embryonic features
• Misidentifications, like endocrine glands

I once made a list of vestigial features across our planet's biota, and I found oodles of them. I'd have to dig up that list, but here are some examples that come to my mind:

• Bird alula or "bastard wing" - a short digit, the thumb
• Mammalian tails, from being much more slender than most other vertebrate tails
• Side digits of hoofed animals, like cows and horses
• Hipbones of cetaceans
• Some parthenogenetic lizards doing "pseudocopulation"
• Aquatic animals laying eggs or giving birth on land, like sea turtles and seals
• Some parthenogenetic plants making flowers, like some dandelions
• Seed plants having multicelled haploid (gametophyte) phases
• Mitochondria and chloroplasts having their own genomes

 

[Swammerdami]

The LUCA is the most recent common ancestor of every cellular organism. It was a full-scale organism, much like present-day methanogens. It had a full-scale DNA-RNA-protein transcription and translation system ...
It's evident that the LUCA had a lot of evolution behind it -- it's rather difficult to imagine direct prebiotic origin for such an organism.

That is where the RNA world comes it. It is an earlier stage where RNA was both information storage and enzyme. Its continued presence and functions are thus vestigial features. BTW, many vestigial features are functional, and they are identified as vestigial by their structure.

To be clear: LUCA seems to have had transcription mechanisms for RNA-->RNA, RNA-->DNA, DNA-->RNA but not for DNA-->DNA. If this seems odd, consider that DNA was a recent invention, and a single copy in a "mother cell" would be enough to keep that cell's genome reliable. When the cell reproduced, RNA would transcribe DNA, constructing a (mutated) copy of the DNA genome. This is assumed because the DNA-->DNA transcription methods are very different between "true bacteria" and archaeotes.

Instead of an RNA world preceding the RNA+Protein world, many theorists suppose that peptide chains co-evolved with RNA. Peptides are useful in catalyzing RNA reactions and vice versa. The very early evolution of the genetic code also supports this model.

Also plausible is a PNA+Protein world preceding RNA+Protein. where PNA is some nucleotide chain more primitive than RNA. Some experiments have shown that a "mash-up" of various types of nucleotide chain might be more effective than an only-RNA source.

This is why I am curious about the timeline of viral evolution WRT LUCA... It would suggest events which would strongly favor the precipitation of RNA encodings of proteins to DNA and the large-scale Exodus from the RNA world.

My understanding WAS that RNA-->DNA "reverse" transcription became obsolete with DNA transcription, and that reverse transcripting viruses (like HIV) might descend from the ancient LUCA RNA-->DNA genes. But then — reviewing the topic of RNA-based Covid vaccines! — I read that some human cells have RNA-->DNA capability. Color me confused.

 

[lpetrich]

To be clear: LUCA seems to have had transcription mechanisms for RNA-->RNA, RNA-->DNA, DNA-->RNA but not for DNA-->DNA.

There is some evidence for that. From 1999,

Did DNA replication evolve twice independently? | Nucleic Acids Research | Oxford Academic

DNA replication is central to all extant cellular organisms. There are substantial functional similarities between the bacterial and the archaeal/eukaryotic replication machineries, including but not limited to defined origins, replication bidirectionality, RNA primers and leading and lagging strand synthesis. However, several core components of the bacterial replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus. This is in sharp contrast to the principal proteins involved in transcription and translation, which are highly conserved in all divisions of life. We performed detailed sequence comparisons of the proteins that fulfill indispensable functions in DNA replication and classified them into four main categories with respect to the conservation in bacteria and archaea/eukaryotes: (i) non-homologous, such as replicative polymerases and primases; (ii) containing homologous domains but apparently non-orthologous and conceivably independently recruited to function in replication, such as the principal replicative helicases or proofreading exonucleases; (iii) apparently orthologous but poorly conserved, such as the sliding clamp proteins or DNA ligases; (iv) orthologous and highly conserved, such as clamp-loader ATPases or 3′→5′ exonucleases (FLAP nucleases). The universal conservation of some components of the DNA replication machinery and enzymes for DNA precursor biosynthesis but not the principal DNA polymerases suggests that the last common ancestor (LCA) of all modern cellular life forms possessed DNA but did not replicate it the way extant cells do. We propose that the LCA had a genetic system that contained both RNA and DNA, with the latter being produced by reverse transcription. Consequently, the modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages.

That suggests some a DNA-RNA hybrid genome, with both DNA-to-RNA and RNA-to-DNA transcription. Both Bacteria and Archaea would have evolved separate DNA-to-DNA polymerases.

 

[bilby]

I'm impressed random search could arrive at the marvelous machine which is LUCA.

Impressed is an appropriate response.

Disbelieving, incredulous or shocked would be less reasonable.

Selection is a very powerful engine for generating impressive complexity from randomness.

 

[Jarhyn]

The LUCA is the most recent common ancestor of every cellular organism. It was a full-scale organism, much like present-day methanogens. It had a full-scale DNA-RNA-protein transcription and translation system ...
It's evident that the LUCA had a lot of evolution behind it -- it's rather difficult to imagine direct prebiotic origin for such an organism.

That is where the RNA world comes it. It is an earlier stage where RNA was both information storage and enzyme. Its continued presence and functions are thus vestigial features. BTW, many vestigial features are functional, and they are identified as vestigial by their structure.

To be clear: LUCA seems to have had transcription mechanisms for RNA-->RNA, RNA-->DNA, DNA-->RNA but not for DNA-->DNA. If this seems odd, consider that DNA was a recent invention, and a single copy in a "mother cell" would be enough to keep that cell's genome reliable. When the cell reproduced, RNA would transcribe DNA, constructing a (mutated) copy of the DNA genome. This is assumed because the DNA-->DNA transcription methods are very different between "true bacteria" and archaeotes.

Instead of an RNA world preceding the RNA+Protein world, many theorists suppose that peptide chains co-evolved with RNA. Peptides are useful in catalyzing RNA reactions and vice versa. The very early evolution of the genetic code also supports this model.

Also plausible is a PNA+Protein world preceding RNA+Protein. where PNA is some nucleotide chain more primitive than RNA. Some experiments have shown that a "mash-up" of various types of nucleotide chain might be more effective than an only-RNA source.

This is why I am curious about the timeline of viral evolution WRT LUCA... It would suggest events which would strongly favor the precipitation of RNA encodings of proteins to DNA and the large-scale Exodus from the RNA world.

My understanding WAS that RNA-->DNA "reverse" transcription became obsolete with DNA transcription, and that reverse transcripting viruses (like HIV) might descend from the ancient LUCA RNA-->DNA genes. But then — reviewing the topic of RNA-based Covid vaccines! — I read that some human cells have RNA-->DNA capability. Color me confused.

This is what I was digging for, thanks!

 

[Jarhyn]

I'm impressed random search could arrive at the marvelous machine which is LUCA.

Impressed is an appropriate response.

Disbelieving, incredulous or shocked would be less reasonable.

Selection is a very powerful engine for generating impressive complexity from randomness.

We might have ended up with a better mechanism, but the fact is once one thing evolved that hacked together a metabolic solution, unless a prototype arrived in short order which could outcompete, any runner-up which could out-evolve the "conventional ATP mill" would be out-developed by the SotA conventional ATP mill. It would die out because of the meta-stability of a well tuned but upper-end-limited invention.

So while what we see seems great, there's entirely the possibility it would be shamed by something purpose-built.

Do we see any better metabolic solutions out there in all of life starting to crop up?

 

[Swammerdami]

My understanding WAS that RNA-->DNA "reverse" transcription became obsolete with DNA transcription, and that reverse transcripting viruses (like HIV) might descend from the ancient LUCA RNA-->DNA genes. But then — reviewing the topic of RNA-based Covid vaccines! — I read that some human cells have RNA-->DNA capability. Color me confused.

This is what I was digging for, thanks!

You were digging for — hoping — that I was (colored) confused? .

 

[Jarhyn]

My understanding WAS that RNA-->DNA "reverse" transcription became obsolete with DNA transcription, and that reverse transcripting viruses (like HIV) might descend from the ancient LUCA RNA-->DNA genes. But then — reviewing the topic of RNA-based Covid vaccines! — I read that some human cells have RNA-->DNA capability. Color me confused.

This is what I was digging for, thanks!

You were digging for — hoping — that I was (colored) confused? .

No, more I was digging for fairly solid discussions of LUCA dominance with respect to transcription strategies.

Mostly I'm interested in understanding what breakthroughs allowed LUCA to essentially outcompete every other replicator. Nothing else survived it other than viruses.

 

[Swammerdami]

So while what we see seems great, there's entirely the possibility it would be shamed by something purpose-built.

Do we see any better metabolic solutions out there in all of life starting to crop up?

It's the answer to a different question but isn't photosynthesis the most efficient energy sourcing?

@ lpetrich or anyone :— what are there? about a half dozen source energy mechanisms used by living cells? It would be nice to see a table of key facts.

Evolution of life on Earth can be broken into four phases:

1. The development of LUCA from random organic goo developing in the micropores of alkaline thermal vents.
2. The development of a wide variety of bacteria and archaea from LUCA.
3. The development of the first Eukaryote with mitochondria, a complex cell nucleus, and sexual reproduction.
4. The development of plants, animals, fungus etc. from early Eukaryote.

. . .The evolution just to get to LUCA was huge, and perhaps more impressive than all the rest. The genetic code was already implemented in LUCA with dozens of RNAs and proteins in support and a marvelous ribosome machine. LUCA is also assumed to possess, among other features, an ATP synthase machine similar to (but more primitive than) the one depicted here:

I'm afraid I'll be taking the Pariah's place and branded a Christian or worse. So I'll don my asbestos suit before nailing myself to a cross and admitting that I'm impressed random search could arrive at the marvelous machine which is LUCA.

Don't get me wrong, but like... That's a really sexy animation. I almost touched myself when I saw it.

There's other interesting, quite different animations of ATP synthase at Google Images. As well as gifs of the operation of a ribosome — much more impressive than ATPase.

Not shown in the gif above is that protons are streaming up from the bottom, propelling the rotation as shown.. The manipulations in the upper part of the machine catalyze ADP+P--->ATP. Think of the machine as straddling the poles of a capacitor: it is simply electric current that builds the ATP.

 

[lpetrich]

• Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria - PMC- 2021
• Evolution of Life on Earth: tRNA, Aminoacyl-tRNA Synthetases and the Genetic Code - PMC - 2020
• The replication machinery of LUCA: common origin of DNA replication and transcription - PubMed - 2020
• A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land - PMC - 2004

Comparison to DNA-to-RNA and RNA-to-RNA transcriptases reveals that the DNA-to-DNA one in Archaea is the closest, with the one in Bacteria likely being a replacement of it. The LUCA was like Archaea more than like Bacteria in other ways, with Bacteria thus having some new features.

Another Archaea - Bacteria difference is membrane lipids. Both domains synthesize terpenes, but only Archaea uses them in its membrane lipids. Bacteria use a new feature: fatty acids. So the LUCA likely had Archaea-like terpenes in its membrane lipids.

 

[Swammerdami]

In post-LUCA life, the cell membrane is VERY tight. Even a single proton (H⁺) is unable to pass easily into the cell except via a deliberate channel, e.g. the ATP-synthase machine mentioned above. Electric balance is retained because protons are pumped to the OUTSIDE of the cell by metabolic systems. IOW, the energy produced (in the form of ATP) by incoming protons is balanced by the outgoing protons carrying energy produced by photosynthesis or other metabolism.

But pre-LUCA life didn't need such metabolic proton pumps; the protons arrived "for free" with the acid-alkali gradient in the thermal vents' micropores. Lane et al postulate that LUCA needed leaky membranes so that protons had an easy exit, and electric charge balance could be maintained.

(This round-about "chemiosmotic" approach to ATP creation is ubiquitous in life, and is therefore strong evidence that the model of Lane et al is correct.)

Another Archaea - Bacteria difference is membrane lipids. Both domains synthesize terpenes, but only Archaea uses them in its membrane lipids. Bacteria use a new feature: fatty acids. So the LUCA likely had Archaea-like terpenes in its membrane lipids.

LUCA had leaky membranes, or none at all.

Thus the following events all coincided at roughly the very same key stage ("inflection point") in the evolution of early life:

• The "invention" of DNA. This offered a HUGE boost to genome stability, even if DNA-->RNA-->DNA was used for reproduction instead of the more direct (and very low mutation-rate) DNA-->DNA.
• The division of LUCA into two child cells, one ancestral to all archaeotes, the other ancestral to all "true" bacteria.
• The development of energy-harnessing mechanisms since the "free" energy from the acid-alkali gradient is unavailable outside the micropore.
• The development of leak-proof lipid cell membranes, required when the rocky membranes of the micropore were no longer available.
• The escape of early cells from the vent micropores to "seek fame and fortune" elsewhere in the vast ocean.

 

[Jarhyn]

It's the answer to a different question but isn't photosynthesis the most efficient energy sourcing?

I'm more talking about energy concentration, and to be fair if I understand right, photosynthesis started with pieces of the conventional ATP mill.

But it is not by any necessary means the "most efficient". It's just the most efficient we've observed happening?

it is simply electric current that builds the ATP.

It's amazing that it does this with current.

It's striking that the logistics for transporting chemically packaged energy requires less fixed infrastructure. You can produce a whack of ATP and not really need to have a fragile filament or yeet something unreasonably hard and hope you don't miss.

It would be interesting if we could isolate a way to produce a cell like a nerve cell which instead of exposing chemical terminals, exposed it's current potentials.

In post-LUCA life, the cell membrane is VERY tight. Even a single proton (H⁺) is unable to pass easily into the cell except via a deliberate channel, e.g. the ATP-synthase machine mentioned above. Electric balance is retained because protons are pumped to the OUTSIDE of the cell by metabolic systems. IOW, the energy produced (in the form of ATP) by incoming protons is balanced by the outgoing protons carrying energy produced by photosynthesis or other metabolism.

But pre-LUCA life didn't need such metabolic proton pumps; the protons arrived "for free" with the acid-alkali gradient in the thermal vents' micropores. Lane et al postulate that LUCA needed leaky membranes so that protons had an easy exit, and electric charge balance could be maintained.

(This round-about "chemiosmotic" approach to ATP creation is ubiquitous in life, and is therefore strong evidence that the model of Lane et al is correct.)

Another Archaea - Bacteria difference is membrane lipids. Both domains synthesize terpenes, but only Archaea uses them in its membrane lipids. Bacteria use a new feature: fatty acids. So the LUCA likely had Archaea-like terpenes in its membrane lipids.

LUCA had leaky membranes, or none at all.

Thus the following events all coincided at roughly the very same key stage ("inflection point") in the evolution of early life:

• The "invention" of DNA. This offered a HUGE boost to genome stability, even if DNA-->RNA-->DNA was used for reproduction instead of the more direct (and very low mutation-rate) DNA-->DNA.
• The division of LUCA into two child cells, one ancestral to all archaeotes, the other ancestral to all "true" bacteria.
• The development of energy-harnessing mechanisms since the "free" energy from the acid-alkali gradient is unavailable outside the micropore.
• The development of leak-proof lipid cell membranes, required when the rocky membranes of the micropore were no longer available.
• The escape of early cells from the vent micropores to "seek fame and fortune" elsewhere in the vast ocean.

I would propose that it might have been a lifecycle thing.

At the beginning of the exodus from the crucible as it were, there were almost certainly mechanisms for motility, as ATPase is part and parcel with the Cilia motor.

I can see it being quite likely that membrane formation and hardening was likely underway through every generation, not just between the generations, as it would be adaptive towards closing leaks so as to traverse to different pores, possibly ones occurring on different vents that were far away.

Eruption and belchings over time would of course eject bits of vent and some of it's pores elsewhere, and the geometry of how the sea floor cracked would drag cold (and so metabolically slowed, not dead but inactive) RNA life away.

This presents a selection environment for the formation of harder membranes.

This would mean that any mutation of an ATPase precursor would be selected for, especially since the presence of harder membranes would be specifically selected so as to survive traversals.

Low mutation rates were not beneficial anyway at this point, and wouldn't be selected for: few things were eating life and everything was primitive.

Selection pressures would make this pretty much inevitable, just a tiny little step off of routine.

 

[Swammerdami]

Interesting comments, Jarhyn! I'll just comment on this:

Low mutation rates were not beneficial anyway at this point, and wouldn't be selected for: few things were eating life and everything was primitive.

We have lots of computer programmers here; how many have coded Optimization by Simulated Annealing (SA)?
In SA you start with "high temperature" with radical changes (mutations) encouraged; then gradually lower the temperature (mutability) to retain your "winnings," still allowing mutations but at a much lower rate.

Early life mimicked the same SA for its genome! One nucleotide chain ("Peptide nucleic acid"?) proposed for possible pre-RNA life didn't even have a phosphate backbone IIRC and presumably mutated easily. Rapid mutation was useful to explore the space of genes and proteins very quickly.

But as seen above, LUCA had elaborate mechanisms. Implementing the genetic code involved several dozen genes. The ribosome and the ATP-synthase machine are elaborate machines. LUCA had at least a dozen other enzymes. A cell's children would be likely to fail if these mechanisms were degraded by mutations.

In other words, the reliability of genome preservation increased (much as in computerized Simulated Annealing) over the period of earliest life. I do not think it coincidence that the key inflection point in LUCA development occurred between the unreliable RNA-->RNA genome reproduction and the low-mutation DNA-->DNA genome. (If LUCA used DNA-->RNA-->DNA reproduction, perhaps that had the "Goldilocks" intermediate mutation rate for that time!)

(Eukaryotes take better care of their DNA than bacteria do. What are the respective mutation rates?)