Defending the Christian Worldview, Creationism, and Intelligent Design
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Defending the Christian Worldview, Creationism, and Intelligent Design

This is my personal virtual library, where i collect information, which leads in my view to the Christian faith, creationism, and Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity

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Defending the Christian Worldview, Creationism, and Intelligent Design » Various issues » Perguntas ....

Perguntas ....

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101Perguntas .... - Page 5 Empty Re: Perguntas .... Wed Sep 22, 2021 6:39 pm



was it a boat on mount ararat or not ?// there are food remains, it is a boat with pitch on the walls
its just evidence of an ancient boat

1. How could such a structure have been constructed at 13,800 feet in the permanent snow cap? I have snapshots of each wood plank with different cuts. I did count just in the site which Philip Williams visited, over 150 planks of different sizes and cuts. Panda lee reported one plank, in his expedition in 2008, to be 20 meters long. Dispersed and buried in ice deep below the surface. In the access tunnels and wood chambers, there are massive stairs made of wood trunks, each at least with a weight of over 200 lbs, buried in ice. There are huge wood walls impregnated with pitch, and curved, like a boat hull. How was all this constructed up there?

2. How could it have been buried so deep?. Under 20-30 feet of frozen volcanic rock and ice? Sub-freezing temperatures make it virtually impossible to construct a large ship under those conditions.

3. How could it have been made, considering that it is too unstable and dangerous in its location? One site leans precariously on a ledge, another on the side of a glacier slowing moving down the mountain. Large rocks regularly tumble the mountain burying the structure and threatening the life of workers.

4. It is a huge structure. It is in at least two pieces which together appear to be about the size of Noah’s Ark (450 feet long). How could it have been made, dragging that much timber that high, fabricating and assembling all the intricate wooden joints ? is it not too much for this height and temperature?

5. It is too complicated. It has a bowed hull, three decks, numerous square deep wooden joints for square wooden nails, tongue and grooved joined boards with evidence of handcraft: Would it not be too intricate and complex to construct under such difficult conditions?

6. It contains pottery, food remains skeletons of animals and various artifacts of ancient age.

7. If it is of recent construction, why is there surface patina on it which does not exist on recently fabricated boards, and there is no known way to fabricate it?

8. Noah and his family worked on level ground for perhaps 120 years. How could someone build this big ship on a high mountain under these seemingly impossible conditions in the few weeks per year after meltwater stops flowing and before winter snow prevents access to the sites?

Kangaroos, why no evidence of them travelling ?

Flood in archaeology and geology no evidence of simultaneous flood

Noah's flood was worldwide:
There are many extra-biblical evidences that point to a worldwide catastrophe such as a global flood. There are vast fossil graveyards found on every continent and large amounts of coal deposits that would require the rapid covering of vast quantities of vegetation. Oceanic fossils are found upon mountain tops around the world. Cultures in all parts of the world have some form of flood legend. All of these facts and many others are evidence of a global flood.

Five civilizations at the flood event

400 years were time enough to the Tower of Babel

Archaeology does not support that hypothesis neither

Strata are dated at various digs

Historians find evidence of

excavation of the city of Jericho

civilization vanished and the appeared again

aegyptians were some of the best historians of the world. Old kingdom age. Age of the great pyramid builders . How did the pyramids be built ? population problem ?

there should be no humans when the pyramids were built

south America, new and old DNA populations

102Perguntas .... - Page 5 Empty Re: Perguntas .... Tue Oct 12, 2021 7:38 am



Perguntas .... - Page 5 Rsos210664f01

H-element of Titanokorys gainesi gen. et sp. nov., paratype ROMIP 65168. (a) Part; (b) counterpart; (c) close-up of ornamentation, photographed under low-angle light; (d), (e) close-ups of posterolateral margins. Ap, anterolateral processes; Bp bilobate axial posterior region; He, H-element; Lp, posterolateral processes; Mn, medial notch; On, ocular notch; Ri, ridges associated with a reticulated pattern; Sa, sagittal spine; Sl1,2, terminal (Sl1) and medial (Sl2) spines of posterolateral processes; Tu, tubercles; Vm, the ventrolateral margin of H-element. Scale bars: (a,b) = 20 mm; (c,d) = 5 mm.

Perguntas .... - Page 5 Rsos210664f02

Assemblage of Titanokorys gainesi gen. et sp. nov., paratype ROMIP 65741. (a) Overview of slab, showing close association of H-element and partial appendage with an assemblage of Cambroraster falcatus consisting of an H-element and pair of appendages; (b) detail of T. gainesi; (c) close-up of endites from frontal appendage; (d) close-up of endites from frontal appendage of C. falcatus; (e) close-up of anterior margin of H-element, showing ornamentation. Ap, anterolateral processes; EnX, endite no. X; He, H-element; He-C, H-element of C. falcatus; Fa, frontal appendage; Fa-C, frontal appendage of C. falcatus; Ri, ridges associated with a reticulated pattern; Sa, sagittal spine; Se, secondary spines on endites; Sp, spiniform distal endites; Ts, Terminal spine; Tu, tubercles. Scale bars, (a,b) = 20 mm; (c–e) = 5 mm.

Perguntas .... - Page 5 Rsos210664f03

Assemblage of Titanokorys gainesi gen. et sp. nov., holotype ROMIP 65415. (a) Overview of slab, with boxed regions indicating close-ups in other panels, note associated agnostids (Peronopsis cf. columbiensis) possibly feeding on the remains or encrusting biofilms [27]; (b,c) original obliquely preserved H-element, with arrows showing the direction of deformation and dashes indicating sagittal axis of symmetry (b) and hypothetical undeformed version (c) using distort mode in Adobe Photoshop version 21.2.2 (based on the length-width proportions of ROMIP 65168). (d) Close-up of P-element spine; (e) close-up of P-element showing ridges; (f) close-up of bands of gill lamellae; (g,h) appendages and oral cone photographed using different low-angle light orientations to emphasize different details; (i,j) overall view (i) and close-up (j) of the frontal appendage of Cambroraster falcatus, ROMIP 65084, showing comparatively shorter spiniform distal endites and shorter secondary spines on more proximal endites. (k) Line drawing of appendages and oral cone of T. gainesi (from g,h); (l–n) close-ups of frontal appendages using different low-angle light orientations (l, close-up of g; m, close-up of h). Bu; burrow; Gb, gill blade; Ig, individual gill filament; In, Indeterminate; Oc, oral cone; Pc, Peronopsis cf. columbiensis; Pd, peduncle (podomere 1); Pe, P-element; PoX, podomere no. X; Ps, P-element spine; other abbreviations see figures 1 and 2. Scale bars: (a–c) = 50 mm; (e,g–i,k–n) = 10 mm; (d,f,j) = 5 mm.

Perguntas .... - Page 5 Rsos210664f04

H-elements of Titanokorys gainesi gen. et sp. nov. showing ornamentation. (a,b) Paratype ROMIP 65749; (a) overview, note associated ptychopariid trilobites; (b) close-up of boxed region from (a); (c,d) paratype ROMIP 65748; (c) overview photographed under low-angle light; (d) close-up of boxed region in (c) showing tuberculate margin. For abbreviations, figure 1. Scale bars = 10 mm.

Perguntas .... - Page 5 Rsos210664f06

Comparative morphology of Pahvantia hastata. (a–c), P. hastata KUMIP 314089; (a), the part showing distal ends of broken endites to the left of the gill blades; (b) part and counterpart superposed to show the nearly complete appendage partly overlying the gill blades, lower inset showing complete counterpart with carapace elements, upper inset showing a close-up of partial appendage and gills on counterpart; (c) counterpart superposed on line drawing of part; (d) appendage of Hurdia for comparison, ROMIP 59259; (e–h), disarticulated Hurdia assemblages, showing groups of connected gill blades associated with other body parts; (e,f), ROMIP 60031; (g,h), ROMIP 60041. Scale bars: (a–c) = 2 mm; (b); upper inset, 5 mm; lower inset, 10 mm; (d–h) = 10 mm. Ds, dorsal spine; Ot, Ottoia prolifica; PEn, peduncular endite, other abbreviations see figures 1 and 3. (a–c) Images courtesy Rudy Lerosey-Aubril.

103Perguntas .... - Page 5 Empty Re: Perguntas .... Thu Nov 11, 2021 2:03 pm



Environmental adaptive pressures in the ocean remain largely the same. There are variegated eco-systems, but all fish have to adapt to live in the ocean, in salty water. Deep-sea creatures living thousands of meters below the ocean surface are exposed to darkness and heavy bone-crushing pressures of the weight of water

Social effects of evolutionary theory

The promotion of materialism
Darwins Theory of evolution paved the way to introduce philosophical naturalism into science. Richard Dawkins wrote: Although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist.

Before the Theory of evolution was popularized in the 19th century, the major figures advancing science were Christians. They are the true science fathers. Bacon, for example, set out the first conception of the scientific method, firmly based on experimental evidence and inductive reasoning.

Faith in evolution diminishes faith in the Bible, the existence of God, and the Genesis account
Creationist and evolutionist positions are by many perceived and portrayed as mutually exclusive and diametrically opposed. The greatest impact is on the Christian faith, whose very foundation was shaken, from the creation of man and the world, the fall of man, and redemption. The rejection of a teleological view of nature, the attack on natural theology, or the depiction of man as merely an advanced ape.  Many justify evolution to deny the existence of a supreme being, an afterlife, and spiritual rewards. most studied by researchers.

Scientific racism

Perceptions of race and ethnicity.
An evolutionary perspective was used to highlight racial differences, and to prove the inferiority of those that are phenotypically different. The drawing trees of life led Ernst Haeckel into believing in the evolution of a Germanic super-race.
He wrote: “if one must draw a sharp boundary, it has to be drawn between the most highly developed and civilised man on one hand, and the rudest savages on the other, and the latter have to be classed with the animals”.

The historical evidence is overwhelming that human evolution was an integral part of Nazi racial ideology. It held a prominent place in the Nazi school curriculum and in training courses in the Nazi worldview. Nazi officials and SS anthropologists agreed that humans, including the Nordic race, had evolved from primates. They believed that the Nordic race had evolved to a higher level of intelligence, physical prowess, and social solidarity than other races, in large part because they had faced what biologists today would call greater selective pressure.

In Nazi Germany, the Darwinist idea of evolution through struggle was taken up in order to prove that the superior pure races would prevail over the mixed inferior ones. Racial thinking facilitated the rise of  political anti-Semitism. Racism indicated that the Jews were not just a religious community but biologically different from other races. 

How can one explain the enthusiastic reception of Blavatsky's ideas by significant numbers of Europeans and Americans from the 1880s onwards? Theosophy offered an appealing mixture of ancient religious ideas and new concepts borrowed from the Darwinian theory of evolution and modern science. This syncretic faith thus possessed the power to comfort certain individuals whose traditional outlook had been upset by the discrediting of orthodox religion

Human zoos

Social Darwinism
an idea popular in the 19th century that holds that "the survival of the fittest" explains and justifies differences in wealth and success among societies and people.

The value and dignitiy of human life
Without God, there can be no intrinsic, sanctity, or inherent value of human life, there can be no measure to distinguish why a cockroach is less valuable than man.  

which claimed that human civilization was subverting natural selection by allowing the "less fit" to survive and "out-breed" the "more fit." Later advocates of this theory would suggest radical and often coercive social measures to attempt to "correct" this imbalance.

From Darwin to Hitler by Richard Weikart, Weikart claims that Darwinism's impact on ethics and morality played a key role not only in the rise of eugenics, but also in euthanasia, infanticide, abortion, and racial extermination, all ultimately embraced by the Nazis.

"The cultural consequences of this triumph of materialism were devastating. Materialists denied the existence of objective standards binding on all cultures, claiming that environment dictates our moral beliefs." ... "materialism spawned a virulent strain of utopianism. Thinking they could engineer the perfect society through the application of scientific knowledge, materialist reformers advocated coercive government programs that falsely promised to create heaven on earth."

Lack of purpose in life.
If there is no God, and evolution is true, then life is empty and purposeless, leading to nihilistic pessimism.  If we are just animals; there is no purpose and meaning in life. Then, pain, death, and suffering are a necessary part of life, essential to furthering the evolution of life on this planet. A loving God has no place in such a scenario. Such a scenario robs the sense that there is a “master plan.” from God for each one of us. 

There can be no fundamental meaning, if there is no God which made us for a specific purpose, and if our lives will cease one day to exist. If that is so, the day we cease to exist, even IF there is a God, what we did during our lifetime, will ultimately cease to have a fundamental meaning. It is just a momentary transition out of oblivion into oblivion.

There can be no objective moral values if evolution is true
1. If there is no God, there are no objective moral values, since they are prescribed " ought to be's".
2. If there is no God, then moral values are just a matter of personal opinion, and as such, no objectively or universally valid at all. According to Naturalism/Materialism, any claims of morality have to be relativistic, utilitarian, and/or cultural in basis but *not* intrinsic or transcendent.
3. If that is the case, unbelievers have no moral standard to judge anything as morally good or bad.
4. Therefore, in order to criticize God, they need to borrow from the theistic worldview, and as such, their criticism is self-contradicting and invalid.
5. Even IF they could make a case to criticize God's choices, that would not refute his existence.

104Perguntas .... - Page 5 Empty Re: Perguntas .... Thu May 19, 2022 5:53 am



Science has not even been able to explain the natural origin of the four basic building blocks of life. In the same sense, as the bricks of a house require precise sizes and dimensions, and have to be made in factories, in serial production, usually involving complex manufacturing processes, production lines, compartments, etc. so do the four basic building blocks of life. Carbohydrates, amino acids, nucleotides, and phospholipids in the precise form as used in the cell are not simply encountered naturally in the environment. Cells use complex metabolic pathways to make them, using the molecular machines inside the cells, proteins, and, furthermore, recycle them, and those that have done their job, are disposed of as trash in a complex machine called the proteasome. Proteins can be imagined as tiny self-operating, preprogrammed robots, that are in many cases lined up in a production-line-like manner, similar as in a car factory. The raw materials are imported from the exterior of the cell, entering the metabolism pathway, where one enzyme does the first manufacturing step, handing over the intermediate product to the second, and so forth, going through several steps until the end product is ready to be used wherever it is needed.  In some cases, the intermediate product is toxic to the cell, like producing reactive oxygen species (ROS). The trick to solving this problem is to employ proteins that have more than one reactive center. So the raw product goes in, and the entire process goes through all necessary stages inside the protein, and no intermediate product leaks out to the outside to contaminate the cell. Pretty smart, hah ?!! One of the essential parts of the cell is the cell membrane. It employs phospholipids, and they use in their structure so-called fatty acids.  One of these awe-inspiring nano multistep nanomachines that perform several synthesis processes, making fatty acids, is called Fatty acid synthase. We'll come later to talk about it.

These tiny production lines produce all the cell components. In abiogenesis research, there are two main views about how everything started. One is the metabolism first, and the other is the replicator first scenario. In order to perform metabolism reactions, there is always a team at work. It is a joint venture of several players at work. In the same sense, if a robot in a car factory production line stops to do its job and has a malfunction or damage, the entire production line gets to a halt, so in the cell. These cellular metabolic pathways are composed of interdependent networks. It is an all-or-nothing business. Everything has to work properly, or the cell dies. Obviously, all this high-tech stuff was not extant on early earth, so the question arises: How did it all start?  The four basic building blocks had to be made somehow, alternatively, without having the complex manufacturing steps at hand. So, origin of life (OOL) researchers had to find natural, non-enzymatic processes that could account for the first emergence of these building blocks. As it comes out, all the proposals have failed. Some are invoking the escape excuse that "science is still working on it". But is it really just a matter of time, until a natural explanation will be found? Decades over decades of intensive, multibillion-dollar scientific research all over the globe, and no result yet?

Even if we hypothesize a path of a natural origin of the basic building blocks on the early earth, a very important gap is commonly overlooked, or not mentioned: How do you go from the non-enzymatic, natural emergence of the building blocks, eventually catalyzed by clay and similar sorts, to the synthesis processes in the cell, using information, energy, and molecular machines embedded in complex metabolic pathways, fully protected and encapsulated in a membrane, full of gates, and able to keep out the materials that should not go in, and recognizing and importing those necessary for life? How do you keep a homeostatic milieu? How do you get the complex, highly regulated, orchestrated, and controlled replication process, including all the necessary error-check and repair mechanisms fully in operation ? How do you go from one state of affairs of e prebiotic soup, or hydrothermal vents, or even meteorites in space full of all sorts of amino acids,  to a fully self-replicating cell? 

Many are trying to explain this fact away, claiming that life could have started much simpler. But how much simpler? And what is actually life? What is the threshold and transition point of non-life, to life? Citing Denton, again, he writes:

1. When we see complexification, that is: Interconnecting parts,where the system is greater than the sum of their parts, then it is logical to attribute such actions to an intelligently acting mind with foresight and foreknowledge, and distant goals.
2. Making systems with the hallmark of complexity depends on the careful elaboration and design in detail of many elementary parts and interconnecting them in a meaningful way conferring a specific purpose or function. Not rarely, small changes in one part of the system can cause sudden and unexpected outputs in other parts of the system, system-wide reorganization, or breaking down of the higher function.
3. Random accidents are not the best case-adequate explanation for the origin of emerging properties of a complex system. intelligent design is.

The RNA world
One has to dig deep, to arrive at the bottom of affairs, and there investigate carefully, to try to unravel, and understand what really is going on, what mechanisms are in play, and that can serve as a basis to draw true to the case inferences. Unless this is done, the risk to come to false conclusions is considerable and real.

To put it short. There is no evidence that there were selective forces driving simple molecules like RNA monomers to catenate, polymerize, start to self-replicate, and undergo mutations through natural selection, becoming informative semantophoretic strings bearing the functional equivalent of a computer hard drive.

Astrophysicist Dr. Paul Sutter claimed in a YouTube video:

"It's possible that early life didn't even use proteins or DNA. It's possible that early life only used RNA. This is called the RNA world hypothesis, and it works because RNA is capable of self-replicating. It's capable of catalyzing reactions. But eventually, short RNA strands appear. And then, these short RNA strands start participating in chemical reactions that get ever more complex. And then, slowly over time due to evolutionary pressure, eventually DNA and proteins emerge as more efficient versions of the same basic process." 9

These are the kind of explanations that pop up in science articles with a certain frequency. The RNA world hypothesis has been popular for almost four decades.  It doesn't matter how confidently and enthusiastically, and convincingly the claim is made, this is pseudo-scientific gobbledygook. Ann Gauger from the Discovery Institute gave a good characterization of pseudo-science. She wrote:

" When certain biologists discuss the early stages of life there is a tendency to think too vaguely. They see a biological wonder before them and they tell a story about how it might have come to be. They may even draw a picture to explain what they mean. Indeed, the story seems plausible enough, until you zoom in to look at the details. I don’t mean to demean the intelligence of these biologists. It’s just that it appears they haven’t considered things as completely as they should. Like a cartoon drawing, the basic idea is portrayed, but there is nothing but blank space where the profound detail of biological processes should be."

This modus-operandi stretches out in all evolutionary literature, books, and popular newspaper articles. The crux is in the details. MICHAEL J. BEHE brought it to the point. He wrote:
In order to say that some function is understood, every relevant step in the process must be elucidated. The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon such as sight, or digestion, or immunity, must include a molecular explanation. It is no longer sufficient, now that the black box of vision has been opened, for an ‘evolutionary explanation’ of that power to invoke only the anatomical structures of whole eyes, as Darwin did in the 19th century and as most popularizers of evolution continue to do today. Anatomy is, quite simply, irrelevant. So is the fossil record. It does not matter whether or not the fossil record is consistent with evolutionary theory, any more than it mattered in physics that Newton’s theory was consistent with everyday experience. The fossil record has nothing to tell us about, say, whether or how the interactions of 11-cis-retinal with rhodopsin, transducin, and phosphodiesterase could have developed step-by-step. Neither do the patterns of biogeography matter, or of population genetics, or the explanations that evolutionary theory has given for rudimentary organs or species abundance. 5

Paradoxes of life
Even if there were a bunch of primed, selected nucleotides on early earth, the only trajectory would have been destruction, either through UV light, hydrolysis ( where the polymer strings break apart in the contact with water), or self-decomposition, becoming asphalts. I often cite Steve Benners brilliant science paper: Paradoxes in the Origin of Life. He writes:

An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. The literature reports (to our knowledge) ZERO CONFIRMED OBSERVATIONS where evolution emerged spontaneously from a devolving chemical system. It is impossible for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. 6

105Perguntas .... - Page 5 Empty Re: Perguntas .... Wed May 25, 2022 3:37 pm



The author is a Bible-believing Christian and holds the belief, that the Genesis 1 account is literally true. No compromise. To the science-oriented reader, that might sound a bit shocking. How can an educated person in the 21st century believe in talking snakes, donkeys, and 2000-year-old fairy tales told by uneducated sheep-herders? Has science not overcome this? Don't we know better today? 

Energy ( Glucose ) + matter ( elements) + information ( stored in DNA) = building blocks of life ( amino acids, DNA and RNA, carbohydrates, phospholipids )
Building blocks ( amino acids) + Information = ATP synthase machines
ATP synthase Machines produce ATP energy.
ATP energy + metabolism = Hardware of the cell that stores information, DNA, and RNA
Information + machines =

In order for life to start, you need energy and information to make the building blocks of life in the right specified complex functional form. So you need 1. energy, 2. matter, 3 information ( data) in the process. These building blocks are used to make machines. Information directs the arrangement of the building blocks, in order to make these machines, like ATP synthase, that makes energy in the form of ATP. Energy and other micromachines are required to make the hardware molecule, DNA, that stores the software, that instructs how to make the machines that make energy, and the hardware to store information. Metabolic pathways make the building blocks. Energy is consumed in the process. Information is required in the process.

This is a circle that has no beginning, and no end. Either all of this started fully operational and ready, or it would have never started.  

In order to make the complex building blocks of life, the elements that make them must be available in a useful form. Carbon, Nitrogen, Phosphorus, Sulfur. They can only be available to the cell if energy cycles are in place. These energy cycles depend on specialized bacteria. So life is necessary to make the elements, that are necessary to have life. Another cycle had to be fully set up to start everything. A stepwise, gradual evolutionary process, is not possible to achieve that state of affairs.

This is a circle that has no beginning, and no end. Either all of this started fully operational and ready, or it would have never started.  

How were the 20 proteinogenic amino acids selected on early earth?
Science is absolutely clueless about how and why specifically this set of amino acids is incorporated into the genetic code to make proteins. Why 20, and not more or less? ( in some rare cases, 22) considering that many different ones could have been chosen? Stanly Miller wrote in the  science paper from 1981: Reasons for the Occurrence of the Twenty Coded Protein Amino Acids:

There are only twenty amino acids that are coded for in protein synthesis, along with about 120 that occur by post-translational modifications. Yet there are over 300 naturally-occurring amino acids known, and thousands of amino acids are possible. The question then is - why were these particular 20 amino acids selected during the process that led to the origin of the most primitive organism and during the early stages of Darwinian evolution. Why Are beta, gamma and theta Amino Acids absent? The selection of a-amino acids for protein synthesis and the exclusion of the beta, gamma, and theta amino acids raises two questions. First, why does protein synthesis use only one type of amino acid and not a mixture of various α, β, γ, δ… acids? Second, why were the a-amino acids selected? The present ribosomal peptidyl transferase has specificity for only a-amino acids. Compounds with a more remote amino group reportedly do not function in the peptidyl transferase reaction. The ribosomal peptidyl transferase has a specificity for L-a-amino acids, which may account for the use of a single optical isomer in protein amino acids. The chemical basis for the selection of a-amino acids can be understood by considering the deleterious properties that beta, theta, and gamma-amino acids give to peptides or have for protein synthesis. 1

The question is not only why not more or less were selected and are incorporated in the amino acid "alphabet", but also how they could/would have been selected from a prebiotic soup, ponds, puddles, or even the archaean ocean?
The ribosome core that performs the polymerization, or catenation of amino acids, joining one amino acid monomer to another,  the ribosomal peptidyl transferase center, only incorporates alpha-amino acids, as Joongoo Lee and colleagues explain in a scientific article from 2020:

Ribosome-mediated polymerization of backbone-extended monomers into polypeptides is challenging due to their poor compatibility with the translation apparatus, which evolved to use α-L-amino acids. Moreover, mechanisms to acylate (or charge) these monomers to transfer RNAs (tRNAs) to make aminoacyl-tRNA substrates is a bottleneck. The shape, physiochemical, and dynamic properties of the ribosome have been evolved to work with canonical α-amino acids 11

There are no physical requirements that dictate, that the ribosome should/could not be constructed capable to incorporate β, γ, δ… amino acids. Indeed, scientists work on polymer engineering, designing ribosomes that use an expanded amino acid alphabet. A 3D printer uses specifically designed polyester filaments to be fed with, that can process them, and print various objects based on the software information that dictates the product form. If someone tries to use raw materials that are inadequate, the printer will not be able to perform the job it was designed for. The ribosome is a molecular 3D nano printer, as Jan Mrazek and colleagues elucidate in a science paper published in 2014

Structural and functional evidence point to a model of vault assembly whereby the polyribosome acts like a 3D nanoprinter to direct the ordered translation and assembly of the multi-subunit vault homopolymer, a process which we refer to as polyribosome templating. 12 where the reaction center is also specifically adjusted to perform its reaction with the specific set of α-amino acids. 

The materials that the machine is fed with, and the machine itself have both to be designed from scratch, in order to function properly. One cannot operate with the adequacy of the other. There is a clear interdependence that indicates that the amino acid alphabet was selected to work with the ribosome as we know it.

From Georga Tech:
The preference for the incorporation of the biological amino acids over non-biological counterparts also adds to possible explanations for why life selected for just 20 amino acids when 500 occurred naturally on the Hadean Earth.
“Our idea is that life started with the many building blocks that were there and selected a subset of them, but we don’t know how much was selected on the basis of pure chemistry or how many biological processes did the selecting. Looking at this study, it appears today’s biology may reflect these early prebiotic chemical reactions more than we had thought,” said Loren Williams,  professor in Georgia Tech’s School of Chemistry and Biochemistry 

The authors mention 500 supposedly extant on early earth. Maybe they got that number from a scientific article about nonribosomal peptides (NRPs) which coincides with that number of 500. Areski Flissi and colleagues write:

Secondary metabolites (nonribosomal peptides) are produced by bacteria and fungi. In fact, >500 different building blocks, called monomers, are observed in these peptides, such as derivatives of the proteinogenic amino acids, rare amino acids, fatty acids or carbohydrates. In addition, various types of bonds connect their monomers such as disulfide or phenolic bonds. Some monomers can connect with up to five other monomers, making cycles or branches in the structure of the NRPs. 5

Stuart A. Kauffman and colleagues published a paper in 2018, which gives us an entirely different perspective. They wrote on page 22, in the section Discussion:

Using the PubChem dataset and the Murchison meteorite mass spectroscopy data we could reconstruct the time evolution and managed to calculate the time of birth of amino acids, which is about 165 million years after the start of evolution. ( They mean after the Big Bang)  a mere blink of an eye in cosmological terms. All this puts the Miller-Urey experiment in a very different perspective. the results suggest that the main ingredients of life, such as amino acids, nucleotides and other key molecules came into existence very early, about 8-9 billion years before life. 6

Why should the number of possible amino acids on early earth be restricted to 500? In fact, as Allison Soult, a chemist from the University of Kentucky wrote: Any ( large ) number of amino acids can possibly be imagined.  7 This number is defacto limitless. The universe should theoretically be able to produce an infinite number of different amino acids. The AA R sidechains can have any isomer combination. They can come right-handed, or left-handed, with one or two functional groups, with cyclic (cyclobutane, cyclopentane, and cyclohexane) and/or branched structures, they can come amphoteric, with different charges, and so on. Furthermore: A carbon atom bonded to a functional group, like carbonyl,  is known as the α carbon atom. The second is β (α, β, γ, δ…) and so on, according to the Greek alphabetical order. It is conceivable that the protein alphabet would be made of β peptides. There is nothing that physically constrains or limits amino acids to have different configurations. In fact, we do know bioactive peptides that use β-amino acids do form polymer sequences 3  Every synthetic chemist will confirm this. There is also no plausible reason why only hydrogen, carbon, nitrogen, oxygen, and sulfur should/could be used in a pool of 118 elements extant in the universe. If the number of possible AA combinations to form a set is limitless, then the chance of selecting randomly a specific set of AAs for specific functions is practically zero. It would have never happened by non-designed means. 

Optimality of the amino acid set that is used to encode proteins 
In 2011, Gayle K. Philip published a science paper, titled: Did evolution select a nonrandom "alphabet" of amino acids? They wrote in the abstract:

The last universal common ancestor of contemporary biology (LUCA) used a precise set of 20 amino acids as a standard alphabet with which to build genetically encoded protein polymers. Many alternatives were also available, which highlights the question: what factors led biological evolution on our planet to define its standard alphabet? Here, we demonstrate unambiguous support that the standard set of 20 amino acids represents the possible spectra of size, charge, and hydrophobicity more broadly and more evenly than can be explained by chance alone. 2

We know that conscious intelligent agents with foresight are able to conceptualize and visualize apriori, a system of building blocks, like Lego bricks, that have a set of properties that optimally perform a specific function or/and task, that is intended to be achieved, and subsequently, we know that intelligent agents can physically instantiate the physical 3D object previously conceptualized. 

Lego bricks in their present form were launched in 1958. The interlocking principle with its tubes makes it unique and offers unlimited building possibilities. It's just a matter of getting the imagination going – and letting a wealth of creative ideas emerge through play. 8

Amino acids are analogous to Lego bricks. Bricks to build a house are made with the right stability, size, materials, and capacity of isolation for maintaining adequate narrow-range temperatures inside a house. Glass is made with transparency to serve as windows.  (Rare earth) Metals, plastic, rubber, etc. are made to serve as building blocks of complex machines. A mix of atoms will never by itself organize to become the building blocks of a higher-order complex integrated system based on functional, well-integrated, and matching sub-parts. But that is precisely what nature needs in order to complexify into the integrated systems-level organization of cells and multicellularity. We know about the limited range of unguided random processes. And we know the infinite range of engineering solutions that capable intelligent agents can instantiate. 

Gayle K. Philip continues:
We performed three specific tests: we compared (in terms of coverage) (i) the full set of 20 genetically encoded amino acids for size, charge, and hydrophobicity with equivalent values calculated for a sample of 1 million alternative sets (each also comprising 20 members)  results showed that the standard alphabet exhibits better coverage (i.e., greater breadth and greater evenness) than any random set for each of size, charge, and hydrophobicity, and for all combinations thereof. Results indicate that life genetically encodes a highly unusual subset of amino acids relative to any random sample of what was prebiotically plausible. A maximum of 0.03% random sets out-performed the standard amino acid alphabet in two properties, while no single random set exhibited greater coverage in all three properties simultaneously. These results combine to present a strong indication that the standard amino acid alphabet, taken as a set, exhibits strongly nonrandom properties. Random chance would be highly unlikely to represent the chemical space of possible amino acids with such breadth and evenness in charge, size, and hydrophobicity (properties that define what protein structures and functions can be built). It is remarkable that such a simple starting point for analysis yields such clear results.

If the set does exhibit nonrandom properties, and random chance is highly unlikely, where does that optimality come from? It cannot be due to physical necessity. Matter has not the necessity to instantiate, to sort out a set of building blocks for distant goals. Evolution and natural selection is a hopelessly inadequate mechanism that was not at play at that stage. The only option left is intelligent design.

Later, in 2015, Melissa Ilardo and colleagues echoed Gayle K. Philip in the paper: Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids. They wrote:

We compared the encoded amino acid alphabet to random sets of amino acids. We drew 10^8 random sets of 20 amino acids from our library of 1913 structures and compared their coverage of three chemical properties: size, charge, and hydrophobicity, to the standard amino acid alphabet. We measured how often the random sets demonstrated better coverage of chemistry space in one or more, two or more, or all three properties. In doing so, we found that better sets were extremely rare. In fact, when examining all three properties simultaneously, we detected only six sets with better coverage out of the 10^8 possibilities tested. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set. 9

That's pretty impressive and remarkable. That means, that only one in 16 million sets is better suited for the task. The most recent paper to be mentioned was written by Andrew J. Doig in 2016. He wrote:

Why the particular 20 amino acids were selected to be encoded by the Genetic Code remains a puzzle. They were selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets. Factors to take into account when assessing why a particular amino acid might be used include its component atoms, functional groups, biosynthetic cost, use in a protein core or on the surface, solubility and stability. Applying these criteria to the 20 standard amino acids, and considering some other simple alternatives that are not used, we find that there are excellent reasons for the selection of every amino acid. Rather than being a frozen accident, the set of amino acids selected appears to be near ideal.10

The last sentence is remarkable. "the set of amino acids selected appears to be near ideal." It remains a puzzle as so many other things in biology that find no answer by the ones that build their inferences on a constraint set of possible explanations, where an intelligent causal agency is excluded a priori. Selecting things for specific goals is a conscious process, that requires intelligence. Attributes, that chance alone lacks, but an intelligent creator can employ to create life.

Biosynthetic cost: Protein synthesis takes a major share of the energy resources of a cell [12]. Table 1 shows the cost of biosynthesis of each amino acid, measured in terms of number of glucose and ATP molecules required. These data are often nonintuitive. For example, Leu costs only 1 ATP, but its isomer Ile costs 11. Why would life ever therefore use Ile instead of Leu, if they have the same properties? Larger is not necessarily more expensive; Asn and Asp cost more in ATP than their larger alternatives Gln and Glu, and large Tyr costs only two ATP, compared to 15 for small Cys. The high cost of sulfur-containing amino acids is notable.

This is indeed completely counterintuitive and does not conform with naturalistic predictions.

Burial and surface: Proteins have close-packed cores with the same density as organic solids and side chains fixed into a single conformation. A solid core is essential to stabilise proteins and to form a rigid structure with well-defined binding sites. Nonpolar side chains have therefore been selected to stabilise close-packed hydrophobic cores. Conversely, proteins are dissolved in water, so other side chains are used on a protein surface to keep them soluble in an aqueous environment.

The problem here is that molecules and an arrangement of correctly selected varieties of amino acids would bear no function until life began. Functional subunits of proteins, or even fully operating proteins on their own would only have a function after life began, and the cells intrinsic operations were on the go. It is as if molecules had the inherent drive to contribute to life to have a first go, which of course is absurd. The only rational alternative is that a powerful creator had the foresight, and knew which arrangement and selection of amino acids would fit and work to make life possible.

Which amino acids came first? It is plausible that the first proteins used a subset of the 20 and a simplified Genetic Code, with the first amino acids acquired from the environment.

Why is plausible? It is not only not plausible, but plain and clearly impossible. The genetic code could not emerge gradually, and there is no known explanation for how it emerged. The author also ignores that the whole process of protein synthesis requires all parts in the process fully operational right from the beginning. A gradual development by evolutionary selective forces is highly unlikely.

Energetics of protein folding: Folded proteins are stabilized by hydrogen bonding, removal of nonpolar groups from water (hydrophobic effect), van der Waals forces, salt bridges, and disulfide bonds. Folding is opposed by loss of conformational entropy, where rotation around bonds is restricted, and introduction of strain. These forces are well balanced so that the overall free energy changes for all the steps in protein folding are close to zero.

Foresight and superior knowledge would be required to know how to get a protein fold that bears function, and where the forces are outbalanced naturally to get an overall energy homeostatic state close to zero.

1. S L Miller: Reasons for the occurrence of the twenty coded protein amino acids 1981
2. Gayle K. Philip: Did evolution select a nonrandom "alphabet" of amino acids? 2011 Mar 24
3. Chiara Cabrele: Peptides Containing β-Amino Acid Patterns: Challenges and Successes in Medicinal Chemistry September 10, 2014
4. Pre-Life Building Blocks Spontaneously Align in Evolutionary Experiment
5. Areski Flissi: Norine: update of the nonribosomal peptide resource
6. Stuart A. Kauffman: Theory of chemical evolution of molecule compositions in the universe, in the Miller-Urey experiment and the mass distribution of interstellar and intergalactic molecules  30 Nov 2019
9. Melissa Ilardo: Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids 24 March 2015
10. Andrew J. Doig: Frozen, but no accident – why the 20 standard amino acids were selected 2 December 2016
11. Joongoo Lee: Ribosome-mediated polymerization of long chain carbon and cyclic amino acids into peptides in vitro 27 August 2020
12. Jan Mrazek: Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles 2014 Oct 30

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Jean Lehmann (24 March 2022): The degeneracy of the genetic code confers a wide array of properties to coding sequences.  The second position of the anticodon–codon interaction is a critical parameter controlling the extent of non-specific pairings accepted at the third position by the ribosome, a flexibility at the root of degeneracy. That residue A1493 of the decoding center provides a significant contribution to the stability, revealing that the ribosome is directly involved in the establishment of degeneracy. The A1493 and A1492 establish the basis of degeneracy when an elementary kinetic scheme of translation is prevailing. The translation of genetic information relies on base pairing between anticodons and codons. While the first two codon positions are restricted to canonical Watson–Crick base pairs, some flexibility occurs at the third position. This flexibility was postulated by F. Crick in 1966 to account for the observed degeneracy in the genetic code, which had just been fully deciphered. He suggested that G could base pair not only with C but also with U if some base displacement was possible at the third position, a possibility coined the ‘wobble hypothesis'. This flexibility would allow reduced sets of tRNAs to translate all amino-acid encoding codons, thereby making translation more efficient. The reason why unspecific pairing can be accepted at the third position became apparent only about 35 years later when the first structures at atomic resolution of the 30S subunit co-crystallized with mRNA fragments and anticodon stem-loops were elucidated. These structures revealed that, unlike at the first and second positions, the ribosome does not structurally constrain the wobble position, implying that some flexibility in the geometry of base pairing is possible.

In the meantime, it was discovered that extended wobbling, called ‘superwobbling’, can also occur at the third position. In that case, an unmodified U (exceptionally an A) at position 34 of a tRNA can base pair with any base at the third position of the codons. So far, superwobbling has been observed only in mitochondria, chloroplasts and other small genome entities with reduced sets of tRNAs. In such cases, the extent of wobbling matches the degeneracy families associated with each of the 16 N1N2 codon doublets of the genetic code: all codons of any codon family, whether it is two- or four-fold degenerate, are translated by a single tRNA through wobbling and superwobbling, respectively.

The rationale behind the existence of these two degeneracy families was partially unraveled in 1978 by U. Lagerkvist, who noticed that the strength of the base pairs in positions 1 and 2 of the codons and the purine/pyrimidine nature of the base at the second position constituted a set of three criteria (or parameters) with which a complete categorization of the 16 codon doublets into the two degeneracy families was possible, a feature that can be highlighted by a symmetry in the genetic code table. Based on the then available structural organization of the decoding center, and the architecture of the anticodon loop, an interpretation of these parameters was proposed in 2008. The analysis  demonstrated that all three parameters of Lagerkvist determine the number of hydrogen bonds contributing to the stability of the WC geometry of the base pair at the second position of the anticodon (N35-N2) 19

‘Snooze button’ on biological clocks improves cell adaptability
Vanderbilt University (2013): The circadian clocks that control and influence dozens of basic biological processes have an unexpected “snooze button” that helps cells adapt to changes in their environment. At least some species can alter the way that their biological clocks function by using different “synonyms” that exist in the genetic code. This provides organisms with a novel and previously unappreciated mechanism for responding to changes in their environment. Like many written languages, the genetic code is filled with synonyms: differently spelled “words” that have the same or very similar meanings. For a long time, biologists thought that these synonyms, called synonymous codons, were in fact interchangeable. Recently, they have realized that this is not the case and that differences in synonymous codon usage have a significant impact on cellular processes. While biological clocks are vital to maintaining healthy patterns of sleep, metabolism, physiology and behavior, under certain environmental conditions strict adherence to these rhythms can be disadvantageous. Organisms can ignore the clock under certain circumstances—much like hitting a biological snooze button on the internal timepiece—and enhance their survival in the face of ever-changing circumstances. CCA, CCG and CCC are synonymous codons because they all encode for the same amino acid, proline. It turns out that there is a reason for this redundancy. Some codons are faster and easier for cells to process and assemble into proteins than others. Optimizing all the codons used by the fungal biological clock knocked the clock out, which was totally unexpected! Clock proteins in the fungus are not properly assembled if they are synthesized too rapidly; it’s as if the speed of one’s writing affected our ability to read the text.

In the cyanobacteria, however, a different phenomenon is observed. Researchers optimized the codons in the cyanobacteria’s biological clock. This did not shut the clock down in the algae, but it did have a more subtle, but potentially as profound effect: It significantly reduced cell survival at certain temperatures. The biological clock with optimized codons might work better at lower temperatures. However the substitution also modified the biological clock so it ran with a longer, 30-hour period. When forced to operate in 24-hour daily light/dark cycles, the bacteria with the optimized clock grew significantly slower than “wild-type” cells. In cyanobacteria, it’s as if writing speed changes the meaning. The potential importance of changes in synonymous codon usage in adapting to environmental factors is magnified by the fact that they can influence the operation of biological clocks, which function as a key adaptation to daily environmental rhythms. Biological clocks control and influence dozens of different basic biological processes, including sleeping and feeding patterns, core body temperature, brain activity, hormone production and cell regeneration. It is now clear that variations in codon usage are a fundamental and underappreciated form of gene regulation. 18

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3. Robert Alicki: Information is not physical 11 Feb 2014
21. David Hume:
26. Sedeer el-Showk: The Language of DNA July 28, 2014

1. Paul Davies & Jeremy England:  The Origins of Life: Do we need a new theory for how life began? at 15:30 Life = Chemistry + information  Jun 25, 2021
2. Guenther Witzany: Life is physics and chemistry and communication 2014 Dec 31
3. Robert Alicki: Information is not physical 11 Feb 2014
4. Paul C. W. Davies: The algorithmic origins of life 06 February 2013
5. David L Abel: Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems 2012 Mar 14
6. Albert Voie: Biological function and the genetic code are interdependent 2006
7. Paul Davies: Life force 18 September 1999
8. G. F. Joyce, L. E. Orgel: Prospects for Understanding the Origin of the RNA World 1993
10. Claus Emmeche: FROM LANGUAGE TO NATURE - the semiotic metaphor in biology 1991
11. David L Abel: Three subsets of sequence complexity and their relevance to biopolymeric information 11 August 2005
12. George M Church: Next-generation digital information storage in DNA 2012 Aug 16
13. Richard Dawkins on the origins of life (1 of 5) Sep 29, 2008
14. Leroy Hood: The digital code of DNA 2003 Jan 23
15. Hubert P. Yockey: Information Theory, Evolution, and the Origin of Life 2005
16. David L. Abel: The Capabilities of Chaos and Complexity 9 January 2009
17. Peter R. Wills: DNA as information 13 March 2016
18. Paul Davies: The Origin of Life January 31, 2003
19. Sergi Cortiñas Rovira: Metaphors of DNA: a review of the popularisation processes  21 March 2008
20. Massimo Pigliucci:  Why Machine-Information Metaphors are Bad for Science and Science Education 2010
21. David Hume:
22. Barry Arrington A Dog Is A Chien Is A Perro Is A Hund February 11, 2013
23. Paul Davies: The secret of life won't be cooked up in a chemistry lab
25. P.Marshall:  Evolution 2.0:Breaking the Deadlock Between Darwin and Design September 1, 2015
26. Sedeer el-Showk: The Language of DNA July 28, 2014
27. Change Laura Tan, Rob Stadler: The Stairway To Life: An Origin-Of-Life Reality Check  March 13, 2020 
28. David L Abel: The Universal Plausibility Metric (UPM) & Principle (UPP) 2009; 6: 27
29. Edward J. Steele: Cause of Cambrian Explosion -Terrestrial or Cosmic? 2018

29. Sir Fred Hoyle: The Universe: Past and Present Reflections November 1981
30. Robert T. Pennock: [size=12]Intelligent Design Creationism and Its Critics: Philosophical, Theological, and Scientific Perspectives 2001
31. Paul Davies: The Origin of Life  January 31, 2003

32. Paul Davies & Jeremy England:  The Origins of Life: Do we need a new theory for how life began? Jun 25, 2021

33. Paul Davies: 'I predict a great revolution': inside the struggle to define life 2019
34. David T.F Dryden: How much of protein sequence space has been explored by life on Earth? 15 April 2008
35. Evolution: Possible, or impossible? Probability and the First Proteins
36. Steve Meyer, Signature in the Cell 2009
37. Hubert P.Yockey: A calculation of the probability of spontaneous biogenesis by information theory 7 August 1977

39. Florian Lauck: Coping with Combinatorial Space in Molecular Design October 2013

40. W.Patrick Walters: Virtual screening—an overview 1 April 1998

41. Brian R. Johnson: Self-organization, Natural Selection, and Evolution: Cellular Hardware and Genetic Software  December 2010

42. Paul Davies: The FIFTH MIRACLE: The Search for the Origin and Meaning of Life  March 16, 2000

43. Daniel J. Nicholson Is the cell really a machine? 4 June 2019

44. MARSHALL W. NIRENBERG Will Society Be Prepared? 11 August 1967

45. Patricia Bralley: An introduction to molecular linguistics Fehruary 1996

46. V A Ratner: The genetic language: grammar, semantics, evolution 1993 May;29

47. Eric Alani: DNA Spell Checkers

48. Libretexts: Genetic Information

49. Richard Dawkins: The blind watchmaker  1 January 1986

50. María A Sánchez-Romero: The bacterial epigenome 2020 Jan;18
51. Daniel J. Nicholson: On Being the Right Size, Revisited: The Problem with Engineering Metaphors in Molecular Biology 2020

1. B.Alberts: Molecular Biology of the Cell. 4th edition. 2003
2. Eugene V. Koonin: Origin and evolution of the genetic code: the universal enigma 2012 Mar 5
9. S J Freeland: The genetic code is one in a million 1998 Sep
10. Shalev Itzkovitz: The genetic code is nearly optimal for allowing additional information within protein-coding sequences 2007 Apr; 17
12. PAUL DAVIES: The Fifth Miracle The Search for the Origin and Meaning of Life 2000
13. H.Yockey: Information theory, evolution, and the origin of life 2005
14. Job Merkel: The Language of DNA 15 NOV, 2019
15. Stephen J. Freeland: Early Fixation of an Optimal Genetic Code 01 April 2000
16. Thomas Butler: Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement 17 June 2009
17. Fazale Rana The Cell's Design: How Chemistry Reveals the Creator's Artistry 1 junho 2008 Page 172:
18. David L. Abel: Redundancy of the genetic code enables translational pausing 2014 Mar 27
21. ULRICH E. STEGMANN: The arbitrariness of the genetic code 9 September 2003
22. L’udmila Lackova: Arbitrariness is not enough: towards a functional approach to the genetic code 2 May 2017
34. B. Alberts Molecular Biology of the Cell 6th ed. 2015
37. D. L. Gonzalez  On the origin of degeneracy in the genetic code 18 October 2019
39. Tessa E.F. Quax: Codon Bias as a Means to Fine-Tune Gene Expression 2016 Jul 16

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(Duplodnaviria)  All viruses of this realm share homologous MCPs (HK97-fold), large and small terminase subunits, prohead maturation proteases and portal proteins, indicating that their morphogenetic modules are monophyletic.

Euryarchaeota and Thaumarchaeota.

Furthermore, the observation that many bacterial members of the Duplodnaviria encode archaeal-like genome replication modules, which are not homologous to the bacterial functional counterparts, also argues in favour of the origin of this virus group antedating the archaeal–bacterial divide. The second realm of dsDNA viruses, Varidnaviria, is represented in prokaryotes by four families of bacterial viruses (Tectiviridae, Corticoviridae, Autolykiviridae and Finnlakeviridae), one family of archaeal viruses (Turriviridae) and the family Sphaerolipoviridae, in which different genera include viruses infecting either bacteria or archaea. However, mining metagenomic data for homologues of the DJR MCP using sensitive computational methods resulted in the discovery of a vast diversity of previously unknown viruses of this realm that, in all likelihood, infect prokaryotes. Actual host assignments await but some of these virus genomes were found in geothermal habitats, strongly suggesting archaeal hosts. 

proviruses encoding DJR MCPs, which has substantially expanded the reach of Varidnaviria in both prokaryotic domains. Phylogenetic analysis of the concatenated DJR MCP and genome packaging ATPases of archaeal varidnaviruses suggested coevolution of this group of viruses with the major archaeal lineages rather than recent horizontal transfer from bacteria. Thus, most likely, the LUCA virome also included multiple groups of dsDNA viruses with vertical (both single and double) jelly-roll MCPs. Furthermore, reconstruction of DJR MCP evolution sheds light on the pre-LUCA stages of virus evolution. Among the ssDNA viruses (realm Monodnaviria), only members of a single order, Tubulavirales (until recently known as the family Inoviridae), consisting of filamentous or rod-shaped viruses, appear to be hosted by both bacteria and archaea.

 However, whereas tubulaviruses are ubiquitous in bacteria, their association with archaea was inferred from putative proviruses present in several archaeal lineages, namely methanogens and aenigmarchaea. Such distribution has been judged best compatible with horizontal virus transfer from bacteria to archaea. Given their ubiquity in bacteria, the origin of filamentous bacteriophages concomitantly or soon after the emergence of the last bacterial common ancestor (LBCA) appears likely, whereas their presence in LUCA cannot be ruled out either. Similarly, microviruses with icosahedral capsids and circular ssDNA genomes are nearly ubiquitous in the environment and are genetically highly diverse. Although for the vast majority of these viruses the hosts are unknown, the few known isolates infect broadly diverse bacteria from five different phyla. It is thus likely that microviruses have a long-standing evolutionary history in bacteria, which probably dates back at least to the LBCA.

 In the extant biosphere, RNA viruses dominate the eukaryotic virome but are rare in bacteria (compared with DNA viruses) and unknown in archaea. Bacterial RNA viruses are represented by two families, the positive-sense RNA Leviviridae and dsRNA Cystoviridae. The host range of experimentally identified members of both families is limited to a narrow range of bacteria (almost exclusively Proteobacteria). However, recent metagenomics efforts have drastically expanded the known diversity of leviviruses, indicating that their share in the prokaryotic virome had been substantially under-appreciated. Reverse-transcribing viruses are conspicuously confined to eukaryotes although prokaryotes carry a substantial diversity of non-packaging (that is, non-viral) retroelements, for example, group II introns. The extant distribution of the viruses of the realm Riboviria, with its drastic display of eukaryotic over prokaryotic host ranges, might appear paradoxical given the broadly accepted RNA world concept of the origin of life, implying the early origin of RdRP and reverse transcriptase (RT)  and, as a consequence, the primordial status of RNA viruses. The origin of leviviruses within bacteria is best compatible with their currently characterized distribution and is a distinct possibility.  

Furthermore, unlike the LUCA, for which most evolutionary reconstructions suggest a mesophilic or a moderate thermophilic lifestyle, the last common ancestors of bacteria and archaea are inferred to have been thermophiles or hyperthermophiles. Extremely high temperatures might be restrictive for the propagation of RNA viruses and thus could represent a bottleneck associated with the demise of the ancestral RNA virome (and potentially explain why RNA viruses are unknown in archaea).  Thus, of the realm Riboviriapositive-sense RNA viruses are a putative component of the LUCA virome,  The ancestral status of many archaea-specific virus groups is difficult to ascertain. However, some monophyletic virus assemblages, such as those with spindle-shaped virions, infect hosts from all major archaeal lineages and thus can be traced to the last archaeal common ancestor. Therefore, their presence in the LUCA virome, with subsequent loss in the bacterial lineage, cannot be ruled out either.

Virus evolution before the LUCA 
The reconstruction of the evolutionary paths from ancestral host proteins to viral capsids sheds light on the early stages of evolution of both realms of dsDNA viruses. The DJR MCP of the Varidnaviria appears to be a unique virus feature, with no potential cellular ancestors detected. By contrast, the SJR MCP of numerous RNA viruses that were also acquired by ssDNA viruses through recombination can be traced to ancestral cellular carbohydrate-binding proteins, with several probable points of entry into the virus world. Thus, the DJR MCP, in all likelihood evolved from the SJR MCP early in the evolution of viruses. Remarkably, apparent evolutionary intermediates are detectable in two virus families. Viruses in the family Sphaerolipoviridae encode two ‘vertically’ oriented SJR MCPs that are likely to represent the ancestral duplication preceding the fusion that gave rise to the DJR MCP88–90. The recently discovered archaeal dsDNA viruses in the family Portogloboviridae contain one SJR MCP92 and thus appear to represent an even earlier evolutionary intermediate. Indeed, structural comparisons of the SJR MCPs from RNA and DNA viruses show that the portoglobovirus MCP is most closely related to the MCPs of sphaerolipoviruses. Combined with the inferred presence in the LUCA virome of multiple groups of Varidnaviria, the discovery of the intermediate MCP forms in capsids of extant viruses implies extensive evolution of varidnaviruses predating the LUCA. The families Portogloboviridae and Sphaerolipoviridae appear to be relics of the pre-LUCA evolution of varidnaviruses and, accordingly, must have been part of the LUCA virome. For the members of the second realm of dsDNA viruses, Duplodnaviria, no cellular ancestor was detected in the dedicated comparative analyses of the sequences and structures of virion proteins. However, a recent structural comparison has shown that the main scaffold of the HK97-like MCP belongs to the strand-helix-strand-strand (SHS2) fold (with the insertion of an additional, uncharacterized domain of the DUF1884 (PF08967) family) and appears to be specifically related to the dodecin family of the SHS2-fold proteins. Dodecins are widespread proteins in bacteria and archaea that form dodecameric compartments involved in flavin sequestration and storage and are thus plausible ancestors for the HK97-fold MCP. Although, in this case, there are no detectable evolutionary intermediates among viruses, the inferred presence of multiple groups of duplodnaviruses in the LUCA virome implies that the recruitment of dodecin and the insertion of DUF1884 are ancient events. Consistently, viruses with short tails (podovirus morphology), long non-contractile tails (siphovirus morphology) and long contractile tails (myovirus morphology) are all found in both bacteria and archaea, indicating that the morphogenetic toolkit of viruses with HK97-fold MCPs attained considerable versatility in the pre-LUCA era.

Virus replication modules 
Each virus genome includes two major functional modules, one for virion formation (morphogenetic module) and one for genome replication. The two modules rarely display congruent histories over long evolutionary spans and are instead exchanged horizontally between different groups of viruses through recombination, continuously producing new virus lineages. The morphogenetic modules including the vertical jelly-roll and HK97-fold MCPs can be traced to the LUCA virome. One of the most widespread replication modules in the virosphere is the rolling circle replication endonuclease (RCRE) of the HUH superfamily. Homologous RCREs are encoded by viruses with SJR and DJR MCPs, HK97-like MCPs and morphologically diverse ssDNA viruses and are also found in many families of bacterial and archaeal plasmids and transposons. Thus, RCRE can be confidently assigned to the LUCA virome or mobilome (that is, all the MGEs of the LUCA). Protein-primed family B DNA polymerases (pPolBs) represent another replication module with a broad distribution spanning several families of viruses and non-viral MGEs62. pPolB is present in bacteria-infecting members of the realms Duplodnaviria (phi29-like podoviruses) and Varidnaviria (Tectiviridae, Autolykiviridae and diverse varidnavirus genomes identified in metagenomic data) as well as in several families of archaeal viruses (Halspiviridae, Thaspiviridae, Ovaliviridae and Pleolipoviridae). In phylogenetic analyses, pPolBs split into two separate clades corresponding to bacterial and archaeal viruses, strongly suggesting that they have coevolved with bacterial and archaeal lineages ever since their divergence from the LUCA. Two other key replication proteins that are among the most common in bacterial and archaeal viruses and MGEs are primases of the archaeo-eukaryotic primase (AEP) superfamily and superfamily 3 helicases (S3H). Whereas S3H are exclusive to viruses and MGEs, the viral AEP form specific families that are not closely related to the cellular homologues. Notably, bacteria do not employ AEP for primer synthesis, and thus bacterial viruses could not have recruited this protein from their hosts. Thus, AEP and S3H, along with RCRE and pPolB, appear to represent major components of the replication modules of the LUCA virome. More generally, contemporary duplodnaviruses display a remarkable diversity of genome replication modules, from minimalist initiators that recruit cellular DNA replisomes for viral genome replication to near-complete virus-encoded DNA replication machineries. In many cases, these DNA replication proteins do not have close cellular homologues, suggesting a long evolutionary history within the virus world. Notably, some of the phage proteins, such as helicase loaders, have replaced their cellular counterparts at the onset of certain bacterial lineages for the replication of cellular chromosomes. Although some tailed bacterial dsDNA viruses encode replication factors of apparent bacterial origin, in archaeal duplodnaviruses, the proteins involved in informational processes, including components of the genome replication machinery, DNA repair and RNA metabolism, are of archaeal type, with none of the known archaeal viruses encoding components of the bacterial-type replication machinery. Finally, tailed archaeal viruses carry archaeal or eukaryotic-like promoters, consistent with the fact that none of the known archaeal viruses encode RNA polymerases, further pointing to long-term coevolution with the hosts. These considerations argue against (recent) horizontal transfers of duplodnaviruses between bacteria and archaea accounting for the observed distribution of these viruses, even though some such transfers might have occurred. Thus, analyses of duplodnavirus and varidnavirus genome replication modules complement those of the morphogenetic modules and suggest extensive divergence of both groups of viruses in the pre-LUCA era.

The informal reconstructions attempted here suggest a remarkably diverse, complex LUCA virome. This ancestral virome was likely dominated by dsDNA viruses from the realms Duplodnaviria and Varidnaviria. In addition, two groups of ssDNA viruses (realm Monodnaviria), namely Microviridae and Tubulavirales, can be traced to the LBCA, whereas spindle-shaped viruses, most likely infected the last archaeal common ancestor. The possibility that these virus groups were present in the LUCA virome but were subsequently lost in one of the two primary domains cannot be dismissed. The point of origin of the extant bacterial positive-sense RNA viruses (realm Riboviria) remains uncertain, with both bacterial and primordial origins remaining viable scenarios. Further virus prospecting efforts could shed light on the history of these viruses. Although the inferred LUCA virome in all likelihood did not include members of many extant groups of viruses of prokaryotes, its apparent complexity seems to exceed the typical complexity of well-characterized viromes of bacterial or archaeal species. These observations imply that the LUCA was not a homogenous microbial population but rather a community of diverse microorganisms, with a shared gene core that was inherited by all descendant life-forms and a diversified pangenome that included various genes involved in virus–host interactions, in particular multiple defence systems. 

According to the ‘chimeric’ scenario of virus origins, different groups of viruses evolved through recruitment of cellular proteins as virion components19. Here, we present evidence that — contingent on our mapping of both duplodnaviruses and varidnaviruses to the LUCA virome — several such events occurred in the earliest phase of the evolution of life, from the primordial pool of replicators to the LUCA. Moreover, virus evolution during that early era went through multiple, distinct stages as demonstrated by the reconstructed histories of the capsid proteins of the two realms of dsDNA viruses. The cellular SJR-containing carbohydrate-binding or nucleoplasmin-like proteins (the ancestors of the varidnavirus DJR MCPs) and the dodecins (the ancestors of the duplodnavirus MCPs) belong to expansive protein families that have already undergone substantial diversifying evolution prior to the origins of the two realms of viruses. The respective protein families do not belong to the universal core of cellular life, so their apparent pre-LUCA diversification further emphasizes the substantial pangenomic, organizational and functional complexity of the LUCA. This conclusion is indeed compatible with the previous inferences on the LUCA made from the analysis of coalescence in different families of ancient genes, namely that a common ancestor containing all the genes shared by the three domains of life has never existed108. Straightforward thinking on the LUCA virome might have envisaged it as a domain of RNA viruses descending from the primordial RNA world. However, the reconstructions suggest otherwise, indicating that the LUCA was similar to the extant prokaryotes with respect to the repertoire of viruses it hosted. These findings do not defy the RNA world scenario but mesh well with the conclusion that DNA viruses have evolved and diversified extensively already in the pre-LUCA era. The RNA viruses, after all, might have been the first to emerge but, by the time the LUCA lived, they had already been largely supplanted by the more efficient DNA virosphere. 8

Aude Bernheim (2019): For a microorganism to be protected against a wide variety of viruses, it should encode a broad defense arsenal that can overcome the multiple types of viruses that can infect it. Owing to the selective advantage that defense systems provide, they are frequently gained by bacteria and archaea through horizontal gene transfer (HGT). Faced with viruses that encode counter-defense mechanisms, bacteria and archaea cannot rely on a single defense system and thus need to present several lines of defense as a bet-hedging strategy of survival. Given their selective advantage in the arms race against viruses, one might expect that defense systems, once acquired (either through direct evolution or via HGT), would accumulate in prokaryotic genomes and be selected for. Surprisingly, this is not the case as defense systems are known to be frequently lost from microbial genomes over short evolutionary time scales, suggesting that they can impose selective disadvantages in the absence of infection pressure. Competition studies between strains encoding defense systems, such as CRISPR–Cas or Lit Abi, and cognate defense-lacking strains have demonstrated the existence of a fitness cost in the absence of phage infectionAccess to a diverse set of defense mechanisms is essential in order to combat the enormous genetic and functional diversity of viruses. None of the strains encode all defense systems. However, if these strains are mixed as part of a population, the pan-genome of this population would encode an ‘immune potential’ that encompasses all of the depicted systems. As these systems can be readily available by HGT, given the high rate of HGT in defense systems, the population in effect harbors an accessible reservoir of immune systems that can be acquired by population members. When the population is subjected to infection, this diversity ensures that at least some population members would encode the appropriate defense system, and these members would survive and form the basis for the perpetuation of the population 5

Felix Broecker (2019): Cellular organisms have co-evolved with various mobile genetic elements (MGEs), including transposable elements (TEs), retroelements, and viruses, many of which can integrate into the host DNA. MGEs constitute ∼50% of mammalian genomes, >70% of some plant genomes, and up to 30% of bacterial genomes. The recruitment of transposable elements (TEs), viral sequences, and other MGEs for antiviral defense mechanisms has been a major driving force in the evolution of cellular life. 6

Muller's Ratchet: Another hurdle in the hypothetical origin of life scenarios
E. V. Koonin (2017): Both the emergence of parasites in simple replicator systems and their persistence in evolving life forms are inevitable because the putative parasite-free states are evolutionarily unstable. 3 E. V. Koonin (2016): In the absence of recombination, finite populations are subject to irreversible deterioration through the accumulation of deleterious mutations, a process known as Muller’s ratchet, that eventually leads to the collapse of a population via mutational meltdown. 2

Dana K Howe (2008): The theory of Muller's Ratchet predicts that small asexual populations are doomed to accumulate ever-increasing deleterious mutation loads as a consequence of the magnified power of genetic drift and mutation that accompanies small population size. Evolutionary theory predicts that mutational decay is inevitable for small asexual populations, provided deleterious mutation rates are high enough. Such populations are expected to experience the effects of Muller's Ratchet where the most-fit class of individuals is lost at some rate due to chance alone, leaving the second-best class to ultimately suffer the same fate, and so on, leading to a gradual decline in mean fitness. The mutational meltdown theory built upon Muller's Ratchet to predict a synergism between mutation and genetic drift in promoting the extinction of small asexual populations that are at the end of a long genomic decay process. Since deleterious mutations are harmful by definition, accumulation of them would result in loss of individuals and a smaller population size. Small populations are more susceptible to the ratchet effect and more deleterious mutations would be fixed as a result of genetic drift. This creates a positive feedback loop that accelerates the extinction of small asexual populations. This phenomenon has been called mutational meltdown. From the onset, there would have had to be a population of diversified microbes, not just the population of one progenitor, but varies with different genetic make-ups, internally compartmentalized, able to perform Horizontal Gene Transfer and recombination. Unless these preconditions were met, the population would die. 1

A plurality of ancestors
The origin of life did not coincide with the organismal LUCA; rather, a profound gap in time, biological evolution, geochemical change, and surviving evidence separates the two. After life emerged from prebiotic processes, diversification ensued and the initial self-replicating and evolving living systems occupied a wide range of available ecological niches. From this time until the existence of the organismal LUCA, living systems, lineages and communities would have come and gone, evolving via the same processes that are at work today, including speciation, extinction, and gene transfer.  4

Eugene V. Koonin (2020): The LUCA was not a homogenous microbial population but rather a community of diverse microorganisms, with a shared gene core that was inherited by all descendant life-forms and a diversified pangenome that included various genes involved in virus–host interactions, in particular multiple defense systems. 8

Horizontal Gene transfer, and the Origin of Life
Gregory P Fournier (2015): The genomic history of prokaryotic organismal lineages is marked by extensive horizontal gene transfer (HGT) between groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Mobile genetic elements, including transposons, plasmids, bacteriophage, and self-splicing molecular parasites, have played a crucial role in facilitating the movement of genetic material between organisms. Ancient HGT during Hadean/Archaean times is more difficult to study than more recent transfers, although it has been proposed that its role was even more pronounced during earlier times in life’s history.  

Aude Bernheim (2019): None of the strains encode all defense systems. However, if these strains are mixed as part of a population, the pan-genome of this population would encode an ‘immune potential’ that encompasses all of the depicted systems. As these systems can be readily available by HGT, given the high rate of HGT in defense systems, the population in effect harbors an accessible reservoir of immune systems that can be acquired by population members. When the population is subjected to infection, this diversity ensures that at least some population members would encode the appropriate defense system, and these members would survive and form the basis for the perpetuation of the population 5

Eugene V. Koonin (2014): Recombinases derived from unrelated mobile genetic elements have essential roles in both prokaryotic and vertebrate adaptive immune systems. 7

From the onset, there would have had to be a population of diversified microbes, not just the population of one species of progenitor, but varies with different genetic make-ups, able to perform Horizontal Gene Transfer (HGT) and recombination. Also, there had to be transposons, viral sequences, plasmids, viruses, mobile genetic elements, parasites, etc.  Unless these preconditions were met, the population would go extinct.

Gene regulation
The regulation of genes is essential and performed in all life forms. Genes have to be expressed at the right time and encountered fast and with precision by the cell's machinery. It is often mentioned that genes are analogous to blueprints. A better comparison might be to compare them to books in a library. Each book contains the instructions to make a specific molecular machine, or how to operate the cell. The gene regulatory network compares to library software, to find books on the shelf.  The regulatory circuitry controls how the cell has to operate, and how to respond and adapt to the surrounding environmental conditions. It activates transcription and represses it when needed, and is responsible for forming phenotypes that best adapt to the surrounding environmental conditions. It controls DNA replication, the partition of nascent chromosomes to form daughter cells, and the repair of DNA, among other essential tasks. Obviously, these functions had to be fully functional when life started, since they are indispensable.

1. Dana K Howe Muller's Ratchet and compensatory mutation in Caenorhabditis briggsae mitochondrial genome evolution 2008
2. Eugene V Koonin: Inevitability of Genetic Parasites 2016 Sep 26
3. Eugene V. Koonin: Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states 04 December 2017
4. Gregory P Fournier: Ancient horizontal gene transfer and the last common ancestors 22 April 2015
5. Aude Bernheim The pan-immune system of bacteria: antiviral defence as a community resource 06 November 2019
6. Felix Broecker: Evolution of Immune Systems From Viruses and Transposable Elements 29 January 2019
7. Eugene V. Koonin: Evolution of adaptive immunity from transposable elements combined with innate immune systems December 2014
8. Eugene V. Koonin: [/size]The LUCA and its complex virome [size]14 July 2020

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