Non-Darwinian Wordle

[Jarhyn]

We have lots of computer programmers here; how many have coded Optimization by Simulated Annealing

I couldn't answer from that direction but I can from generalized roguelike gameplay:

Fail faster at the start hang on once you're in.

Decisions closer to the start just don't matter as much and working too hard to retain early failures is just counterproductive.

One good game to play until you win it twice at least, is NOITA.

In the first moments, you scream in with nothing, and take really crazy risks but once you get a few hours in, slowing down and taking your time is much better.

Play NETHACK?
"Let's go, Valkyrie!"
(5 second later) "oops, starved to death, LOL!"
"Let's go, Valkyrie!"
(5 hours later) "oh shit don't let that thing slime me"

It's an emergent strategy in generalized gameplay. There is natural selection pressure that would apply there, as you say.

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

This is a keen insight.

 

[lpetrich]

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

 Photosynthesis and  Electron transport chain and  Chemiosmosis

Photosynthesis was added onto existing electron-transfer metabolism in the form of antenna complexes that energize electrons with absorbed photons.

ATP? Indirect.

Electron-transfer metabolism pumps protons (hydrogen ions) out of a cell, or else into flattened bubbles inside the cell called thylakoids. The protons are allowed to return through ATP-synthase enzyme complexes, and it is those complexes that assemble the ATP.

What is ATP? Adenosine triphosphate, a RNA building block with some extra phosphates added on.

Adenosine:
(adenine) - (ribose)
or for short,
A - R
A. monophosphate (AMP):
A - R - P
A. diphosphate (ADP):
A - R - P - P
A. triphosphate (ATP):
A - R - P - P - P

The P's are phosphate ions, and the energy resides in the P - P bonds.

 

[Hermit]

Typical Christian. Post a bunch of obvious falsehoods, get hammered, and play the victim.

Do you have statistical evidence supporting your assertion that FreethoughtPariah is a typical Christian?

 

[lpetrich]

More on ATP and its relatives.

AMP is what's used in RNA molecules. The others are used for energy.

AMP + Pi <-> ADP
ADP + Pi <-> ATP
(Pi = inorganic phosphate)

Also
ATP -> AMP + P-P (pyrophosphate)

There's a variant of AMP called cyclic AMP that's used for signaling inside of cells.

 

[Swammerdami]

Other miscellaneous comments about ATP:

• Although the total amount of ATP in the human body at any one instant may be smallish, the cycle ATP-->ADP-->ATP repeats more than 1000 times per day. Thus a human produces (and consumes) roughly his own body weight in ATP every day. At 30.5 kJ/mol produced by ATP-->ADP and ATP weight 507.18 g/mol, this works out to about 50 watts of ATP power consumption (and production) by a typical adult human.
  (I calculated that 30.5 kJ/mol works out to 0.32 eV per molecule, about thrice the strength of a hydrogen bond. Does this seem low?)
• Instead of adenosine triphosphate, other nucleosine triphosphates are possible. In particular GTP (guanosine triphosphate) is produced by the citric acid cycle and used extensively to supply energy during ribosome operation. It is unclear to me whether there are ATP<-->GTP transformations, or whether ATP statistics include GTP.
• When growing a new protein, about 5 molecules of ATP or GTP are expended altogether for each amino acid. I think this is the major "energy sink" in the cell. In animal cells at 26°C a ribosome typically grows its protein at about five amino acids per second.
• Magnesium ions are used to bind to negative phosphate ions and catalyze their activity. Thus magnesium is a key component both of ribosomes and of ATP synthase complexes.
• According to Nick Lane, it takes ten protons to drive the ATP-synthase rotating head through one complete turn — that head can spin at over 100 revolutions per second — and that turn produces 3 ATP's. Thus if ATP is the "dollar bill" of cellular energy currency, the pumped proton is a coin worth about 30 cents. (Some sources imply 12 protons per revolution. And surely there is some proton leakage.)

 

[Bomb#20]

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

How could we know that's the case? For all we know the descendants of LUCA and the descendants of its contemporaries may have coexisted for a billion years, with LUCA's descendants gradually becoming more dominant. Maybe the last non-LUCA-derived organisms hung on for eons in niche environments, like tuataras while lizards were taking over the world. It doesn't mean the original Triassic lizard had some breakthrough making it better than the original Triassic pre-tuatara. Whichever capabilities eventually let lizards outcompete tuataras presumably accumulated over two hundred million years.

 

[lpetrich]

ATP is clearly a relic of the RNA world.

Here are some more relics:

 Niacin -- Vitamin B3 -- active forms  Nicotinamide adenine dinucleotide and  Nicotinamide adenine dinucleotide phosphate - has bits of RNA, and the niacin part is like a modified nucleobase. Modified nucleobases are also used in transfer RNA, modified after the the transcription of the RNA.

It's involved in redox metabolism: NAD(P)+ + (2H) -> NAD(P)H + H+

 Riboflavin -- Vitamin B2 -- active forms  Flavin mononucleotide and  Flavin adenine dinucleotide - has bits of RNA, and acts like a modified nucleobase.

FAD and FMN alternate between oxidized and reduced forms: FADH2 and FMNH2

 Pantothenic acid -- Vitamin B5 --  Coenzyme A -- attached at the phosphate end of adenosine.

Bonds with acetate (acetic acid, the vinegar acid).

So electron-transfer metabolism, phosphate energy metabolism, and acetic acid metabolism date back to the RNA world.

 

[lpetrich]

Electron-transfer metabolism also includes:

Quinones:  Coenzyme Q10 and  Plastoquinone - they have a chain of 9 isoprenes, making a long terpene chain.

They work by alternating quinol (reduced) and quinone (oxidized). The two oxygens on its benzene ring alternate -OH (reduced) and =O (oxidized).


The enzyme  Cytochrome (several varieties) -- has a heme group with iron in it.


Tthe enzyme  Ferredoxin -- has iron-sulfur complexes in it, suggesting that a bit of surrounding rock is preserved in that enzyme.


For biosynthesis, I note  Folate -- folic acid -- Vitamin B9 -- related to  Tetrahydrofolic acid and  Tetrahydromethanopterin -- involved in reducing carbon dioxide to methane and methyl groups with hydrogen. That makes this cofactor at least as old as the LUCA.

 

[lpetrich]

• How did LUCA make a living? Chemiosmosis in the origin of life - Lane - 2010 - BioEssays - Wiley Online Library
• How did LUCA make a living? Chemiosmosis in the origin of life - PubMed
• How did LUCA make a living? Chemiosmosis in the origin of life — Nick Lane
  [/quote]
  Multiple links included for the sake of cross-references. Biochemist Nick Lane makes a strong case for fermentation *not* being primordial.
  

  Despite thermodynamic, bioenergetic and phylogenetic failings, the 81-year-old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup is homogeneous in pH and redox poten tial, and so has no capacity for energy coupling by chemiosmosis. Thermodynamic constraints make chemiosmosis strictly necessary for carbon and energy metabolism in all free-living chemotrophs, and presumably the first free-living cells too. Proton gradients form naturally at alkaline hydrothermal vents and are viewed as central to the origin of life. Here we consider how the earliest cells might have harnessed a geochemically created proton-motive force and then learned to make their own, a transition that was necessary for their escape from the vents. Synthesis of ATP by chemiosmosis today involves generation of an ion gradient by means of vectorial electron transfer from a donor to an acceptor. We argue that the first donor was hydrogen and the first acceptor CO2.

  Is fermentation ancestral? A common belief is that it is.
  

  But there are profound difficulties – both chemical and biological – in viewing fermentation as primitive rather than derived. Fermentation is chemically a disproportionation – not a simple redox reaction, in which electrons are stripped from a donor and passed onto an acceptor, driven by strong thermodynamics. In contrast with respiration, the amount of energy released by fermentation is tiny, reflecting its lack of thermodynamic driving force. To tap such an insignificant source of energy requires more rather than less sophistication, and indeed about 12 enzymes are needed to catalyse a complex succession of steps in glycolytic-type fermentations based around the Embden-Meyerhoff pathway. These enzymes are proteins encoded by genes, which would have had to evolve as a functional unit without any other source of energy in the primordial oceans – close to an impossibility in an RNA world, let alone the only way to evolve one.

  Then noting that chemiosmosis is universal and that "pure" fermenters are not early branchers.
  
  "Perhaps most strikingly of all, bacteria and archaea differ markedly in the gene sequences and crystal structures of enzymes that catalyse the individual steps of fermentation."
  
  Which strongly suggests multiple evolution of fermentation.
  
  "Thus RNA, DNA, the universal genetic code, transcription, translation, ribosomes, a rotor-stator-type ATPase, ATP and the Krebs cycle are inherited from LUCA, while traits like oxygenic photosynthesis are not, and evolved later, with the cyanobacteria."
  
  Also the Wood-Ljungdahl biosynthesis pathway for acetic acid. It uses folate and pantothenate.

 

[lpetrich]

"Alkaline hydrothermal vents as the primordial source of energy for life"

Regardless of whether it is produced abiotically or by methanogens deeper within the crust, the methane in alkaline vents gives a clue to the origin of life: life began as a ‘side effect’ of the direct hydrogenation of carbon dioxide, to form methane or acetate. All autotrophs today fix carbon dioxide using hydrogen, either directly or indirectly (from water or other electron donors like H2sS), yet there are only five known primary pathways of carbon dioxide fixation. All except one consume energy (ATP) to fix carbon. The exception is the acetyl CoA (Wood-Ljungdahl) pathway of direct reaction of hydrogen with carbon dioxide.

"The origin of life in alkaline vents"

The energy that runs the motor of life in methanogenic and acetogenic metabolism comes from electron transfer from H2 to CO2. The formation of either methane or acetate from H2 and CO2 releases energy, and it is this energy that methanogens and acetogens harness to fuel all their biosynthetic pathways. A portion of the energy released in the acetyl CoA pathway is captured in the form of the high-energy thioester bond of acetyl CoA. Because of the simplicity of the C1 compound chemistry involved, Fuchs suggested that the acetyl CoA pathway is as ancient as it gets in biochemistry, and this view remains current among microbiologists.

It is noteworthy that methanogens convert two molecules of CO2 to acetyl CoA without the participation of ATP or any other triphosphate. Transition metal sulphides abound in the methanogen version of the acetyl CoA pathway, but the universal energy currency ATP is missing. Instead, thioesters like acetyl CoA are central to the bioenergetics of the most primitive biochemical pathways, and the acetyl CoA pathway is the best example.

This is much like what Gunter Wächtershäuser has been proposing.

 

[lpetrich]

"Chemiosmosis is fundamental and universal"

Noting that Bacteria and Archaea both have chemiosmotic energy metabolism, that their rotor-stator ATP-synthase enzyme complexes have some homologous subunits, and that they both have ferredoxins, quinones, and cytochromes.

"Archaeal membranes are composed of isoprenoid side chains, joined by ether bonds to L-glycerol; bacteria use fatty acids, joined by ester bonds to D-glycerol."

"Likewise the bacterial cell wall is composed of peptidoglycans, usually missing altogether in archaea; or if not, archaeal cell walls lack the typical D -amino acids and N-acetylmuramic acid of bacteria."

Then discussing "The primordial proton-motive force" and concluding that it was a gradient in H⁺ ion concentration in the environment, what one would expect from a hydrothermal vent.

Then "Why chemiosmosis was necessary" and then some conclusions.

 

[lpetrich]

A nice thing about this prebiotic-proton-gradient hypothesis is that it features a prebiotic form of chemical disequilibrium, and disequilibrium is necessary to power metabolism and growth and reproduction. This simplifies the problem of the origin of life, because the earliest organisms can use a pre-existing energy source without a lot of evolution.

 

[Swammerdami]

A nice thing about this prebiotic-proton-gradient hypothesis is that it features a prebiotic form of chemical disequilibrium, and disequilibrium is necessary to power metabolism and growth and reproduction. This simplifies the problem of the origin of life, because the earliest organisms can use a pre-existing energy source without a lot of evolution.

Which came first, the chicken or the egg? Evolution or energy harnessing?

Evolution depends on billions of trillions of experiments, of random searches into the space of possible RNA's. An enormous amount of reproduction and growth was needed to explore that space. And that growth didn't come cheap: To produce a single gram of organic matter to be incorporated into nucleic acid or protein required — especially given the primitive mechanisms of earliest life — producing (and disposing of) a ton of waste material. (The ton/gram ratio is from my unreliable memory, but the ratio is huge.)

So the evolution of even the earliest proto-life (e.g. LUCA) required HUGE amounts of growth; and the growth required HUGE amounts of energy. (And the energy had to be usable free energy, not just heat.) The energy could NOT have come from the sophisticated energy mechanisms of life today, e.g. photosynthesis — It was impossible to develop a photosynthetic "chicken" without the evolutionary "egg."

So, as lpetrich points out, a HUGE source of free energy was necessary for life's early evolution. Does Nick Lane lack imagination when he writes that ONLY the alkaline vents present themselves as a possibility? He mentions lightning in the violent weather of early Earth as another possible energy source, but claims lightning's energy density wasn't enough. (I think lightning has other flaws rendering it unlikely as the main source for early life's energy.)

 

[lpetrich]

Cofactors are Remnants of Life’s Origin and Early Evolution | SpringerLink - at PubMed: Cofactors are Remnants of Life’s Origin and Early Evolution - PMC
noting
Coenzymes as fossils of an earlier metabolic state - cofactors_molecular_fossils.pdf by Harold White

A metabolic system composed of nucleic acid enzymes is proposed to have existed prior to the evolution of ribosomal protein synthesis. Vestiges of these nucleic acid enzymes persist in contemporary coenzymes. This proposal rationalizes the fact that many coenzymes are nucleotides or heterocyclic bases which could be derived from nucleotides.

...
Although there have been discussions of the evolution of coenzymes (Handler, 1963; Eakin, 1963), none have explained the curious fact that many coenzymes are nucleotides (NAD, NADP, FAD, coenzyme A, ATP, etc.) or contain cyclic nitrogenous bases which could be derived from nucleotides (thiamin pyrophosphate, tetrahydrofolate, pyridoxal phosphate, etc.) (Dixon & Webb, 1955).

Back to "Cofactors as remnants".

The RNA World is one of the most widely accepted hypotheses explaining the origin of the genetic system used by all organisms today. It proposes that the tripartite system of DNA, RNA, and proteins was preceded by one consisting solely of RNA, which both stored genetic information and performed the molecular functions encoded by that genetic information. Current research into a potential RNA World revolves around the catalytic properties of RNA-based enzymes, or ribozymes. Well before the discovery of ribozymes, Harold White proposed that evidence for a precursor RNA world could be found within modern proteins in the form of coenzymes, the majority of which contain nucleobases or nucleoside moieties, such as Coenzyme A and S-adenosyl methionine, or are themselves nucleotides, such as ATP and NADH (a dinucleotide). These coenzymes, White suggested, had been the catalytic active sites of ancient ribozymes, which transitioned to their current forms after the surrounding ribozyme scaffolds had been replaced by protein apoenzymes during the evolution of translation. Since its proposal four decades ago, this groundbreaking hypothesis has garnered support from several different research disciplines and motivated similar hypotheses about other classes of cofactors, most notably iron-sulfur cluster cofactors as remnants of the geochemical setting of the origin of life. Evidence from prebiotic geochemistry, ribozyme biochemistry, and evolutionary biology, increasingly supports these hypotheses. Certain coenzymes and cofactors may bridge modern biology with the past and can thus provide insights into the elusive and poorly-recorded period of the origin and early evolution of life.

I found a paper with this whimsical title: The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)a - PMC - an allusion to Winston Churchill's famous quote about democracy.

 

[lpetrich]

What they list: along with ATP and S-adenosylmethionine (SAM), almost every B vitamin.

• B1 - thiamin
• B2 - riboflavin - FAD, FMN
• B3 - niacin - NAD, NADP
• B5 - pantothenic acid - Coenzyme A
• B6 - pyridoxine (-al, -amine)
• B7 - biotin (didn't mention)
• B9 - folic acid
• B12 - cobalamin (didn't mention)

 B vitamins

Biotin has a back-to back pair of rings: C-C-N-C-N and C-C-C-S-C, and B12 has a modified porphyrin ring called a corrin. It also has a modified adenosine in it. Porphyrin is a ring of four C-C-C-C-N rings.

Metabolic complexity in the RNA world and implications for the origin of protein synthesis | SpringerLink

On the basis of codon distributions in the modern genetic code it is argued that the first proteins to have been synthesized and used by ribo-organisms were predominantly hydrophobic and likely to have performed membrane-related functions (such as forming simple pore structures), activities essential for the evolution of membrane-enclosed cells.

 

[lpetrich]

Microorganisms | Free Full-Text | The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors

The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H2, CO2, and ammonia (NH3) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO2 is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO2, and the circumstance that the core’s main products are far more reduced than CO2 indicate that the core arose in a highly reducing environment. The chemical reactions of the autotrophic core suggest that it arose from H2, inorganic carbon, and NH3 in an aqueous environment marked by highly reducing and continuously far from equilibrium conditions. Such conditions are very similar to those found in serpentinizing hydrothermal systems.

I will look in it for identified cofactors.

 

[lpetrich]

If we look at the cofactors required to get from H2 and CO2 to pyruvate in acetogens and methanogens [6,62], we find that methanofuran, NAD(P)H, corrins, coenzyme A, thiamine, flavins, F420, three pterins—folate, methanopterin, and the molybdenum cofactor MoCo—as well as FeS clusters, a prosthetic group of proteins that we count as a cofactor here, are required.

Some of them are specific to methanogens: methanofuran, methanopterin (closely related to folate), coenzyme F420 (a flavin derivative).
MoCo = Molybdopterin

So we get this list down to NAD(P), coenzyme A (CoA), thiamine, flavin (FAD, FMN), folate, porphyrin.

Very surprisingly, only three additional cofactors (biotin, pyridoxal phosphate, and SAM) are required for the synthesis of the 11 other cofactors plus the main nucleosides of nucleic acids and the 20 amino acids, whereby only two more (coenzyme M and coenzyme B) are required specifically in the methanogenic pathway of energy conservation.

 

[lpetrich]

From 1989: Modern metabolism as a palimpsest of the RNA world. | PNAS - the "breakthrough organism" was the last one to use only RNA enzymes (ribozymes).

As reconstructed here, this organism had a complex metabolism that included dehydrogenations, transmethylations, carbon-carbon bond-forming reactions, and an energy metabolism based on phosphate esters. Furthermore, the breakthrough organism probably used DNA to store genetic information, biosynthesized porphyrins, and used terpenes as its major lipid component. This model differs significantly from prevailing models based primarily on genetic data.

RNA cofactors: NAD, SAM, CoA, ATP, FAD

Proposes DNA before proteins, for what seem to me to be weak reasons -- DNA could have been invented between the BO and the LUCA, the Last Universal Common Ancestor, thus keeping its ubiquity.

"The Breakthrough Organism Biosynthesized Tetrapyrroles" - porphyrins and relatives like corrins (in B12) and chlorins (in chlorophyll)

Porphyrins are made from delta-aminolevulinic acid (delta-ALA, a.k.a. 5-ALA).  Aminolevulinic acid and ALA is made by two routes:

Shemin: glycine + succinyl-CoA

C5: glutamyl-tRNA + glutamate-1-semialdehyde
tRNA = transfer RNA

The Shemin pathway is used by alpha-proteobacteria and non-photosynthetic eukaryotes, and in eukaryotes, it is done in mitochondria.

The C5 pathway is used by all other cellular organisms, and in eukaryotes, it is done in chloroplasts.

So the C5 pathway was the ancestral one, and the Shemin one an innovation in some alpha-proteobacterium. One of that organism's descendants was "eaten" by a proto-eukaryote, becoming the first mitochondrion, and taking the genes for Shemin with it. When a descendant of that proto-eukaryote "ate" a cyanobacterium, making it the first chloroplast, that organism took the genes for C5 with it.

Looking further at C5, it uses a transfer RNA and Shemin doesn't. That suggests that C5 may go back all the way to the RNA world.

 

[lpetrich]

"The Breakthrough Organism Did Not Synthesize Fatty Acids" - ordinary bacteria do so, but not archaea. Or it was either lost by the ancestor of Archaea or else gained by the ancestor of Bacteria.

The biosynthesis of fatty acids involves biotin and acyl carrier protein (ACP). Both almost certainly did not arise before translation. ACP is a product of translation; it must have emerged after the breakthrough. Chemical and structural features of biotin, reviewed a decade ago by Visser and Kellogg (22), strongly suggest that biotin arose after protein catalysts.

So biotin does not go back to the RNA world.

"The Breakthrough Organism Synthesized Terpenes" - they are found all over our planet's biota, and one can be confident that the LUCA made terpenes.

We consider the following facts and their implications:

(i) Higher terpenes are biosynthesized via similar routes in all three kingdoms, implying that the progenote biosynthe- sized terpenes, especially higher terpenes (di- and triter- penes).

(ii) In the eubacterium Rhodopseudomonas acidophila, membranes contain terpenoids covalently joined to RNA fragments, which serve as the polar part of the amphiphilic lipid molecule (50).

(iïi) However, RNA is not uniquely suited as a polar group in this capacity. Indeed, in most lipids, polar components are not RNA. This suggests that RNA-conjugated lipids were present in the breakthrough organism.

That seems to me a bit weak, because terpene-RNA bonds might be a quirk of R. acidophila.

But terpenes are a part of ubiquinone and plastoquinone, involved in electron-transfer metabolism, something that likely goes back to the RNA world. So terpenes likely do so also.

I infer that about electron-transfer metabolism, because some other cofactors in it also do so: NAD(P), flavins, porphyrins.

 

[lpetrich]

 Robert Wiedersheim - that article has his big list of 86 putative vestigial features.

Some of them are "real" vestigial features, like wisdom teeth and the appendix.

Some of them are transient embryonic features, like the embryonic tail, which disappears except for the coccyx (tailbone). We also grow vestigial gill arches, though they don't grow into functional gills. They are then either resorbed or reused in various ways. The frontmost one becomes the jaws, for instance. The heart starts off as a two-chambered heart that splits into two two-chambered sub-hearts with four chambers in all. We also go through two sets of kidneys before settling on a third set of kidneys.

Some of them are endocrine glands, like the pituitary gland, and those aren't vestigial at all, but instead without very obvious function.

 Vestigiality and  Human vestigiality - vestigial features often continue to have functions, and it is their structure that marks them out as vestigial.