Do viruses help explain the origin of life?

Do viruses help explain the origin of life?

http://www.uncommondescent.com/intelligent-design/do-viruses-help-explain-the-origin-of-life/

Koonin estimates that the likelihood of life’s evolving anywhere in the observable universe over its 13.8-billion-year lifetime is just 1 in 101,018 – that’s 1 in 1 followed by 1,018 zeroes! And that’s an estimate that Koonin himself describes as generous, in an article he wrote in 2007, titled, The Cosmological Model of Eternal Inflation and the Transition from Chance to Biological Evolution in the History of Life (Biology Direct 2 (2007): 15, doi:10.1186/1745-6150-2-15).

http://www.biologydirect.com/content/2/1/15

In the passage below, the term “O-region” refers to an observable universe, like our own. Koonin considers the emergence of life in our observable universe to be such an unlikely event that he is forced to postulate the existence of a vast and possibly infinite number of universes like our own, in order to make the origin of life somewhere reasonably probable. Even assuming the existence of self-replicating RNA molecules, the difficulty of generating a translation-replication system (which is found in all cellular organisms) by a process of Darwinian selection is truly staggering. As Koonin puts it:

In other words, even in this toy model that assumes a deliberately inflated rate of RNA production, the probability that a coupled translation-replication emerges by chance in a single O-region is P < 10-1018. Obviously, this version of the breakthrough stage can be considered only in the context of a universe with an infinite (or, at the very least, extremely vast) number of O-regions.

Dolja contends that cells could not have evolved without viruses, as they need reverse transcriptase (which is found only in viruses) in order to move from RNA to DNA.

In other words, instead of helping to solve the problem of the origin of life on Earth, recent research has only served to highlight one of its central paradoxes. And yet the science media reports the latest discoveries as if the solution is just around the corner. Don’t you find that just a little strange?

On the Origin of Life

http://www.tomveatch.com/life.html

I'm no professional biochemist, but here's something very
interesting

which I haven't seen anyone explain before. I think that the single, miraculous, random event that keyed L.I.F.E...
is:

reverse transcriptase.
Or, you might say, the random assembly of nucleotides comprising, suddenly, the RNA sequence from which RT is generated. The idea is that...
1) in a puddle of nucleotides, fats, and amino acids, all expectably present in the pre-life Earth environment, carrying out some natural level of protein synthesis weakly and slowly,
2) where the nucleotides in the puddle would combine in random sequences by the weak chemical bonding natural to them, (all expectable), these sequences being small RNAs and DNAs, and
3) where from those RNAs are generated proteins, using the amino acids and the driving energy of day/night cycling (all expectable), then
4) one of the RNA sequences generated was the random RNA which happens to be the one that codes for reverse transcriptase. This event (4) is the key, single, almost-but-not-actually-miraculous, random event in the creation of life according to this view. Then,
5) that RNA produced one or more reverse transcriptases using the protein synthesis going on in the puddle, and
6) the reverse transcriptase started doing its wonderful thing, which is generating a lot of DNAs from the nearby RNAs, and it's no miracle that that would include the DNA that its own RNA conceptually determines,
7) I have to wave my hands about the transcription of DNAs to RNAs, because now we have DNAs and need to get to the same RNA again, but once we get that, then
8 ) an extra copy of the RNA for reverse transcriptase appears having been transcribed from that DNA. Presto, reproduction.
8  ) Lots of copies of reverse transcriptase and its RNA and DNA can quite reasonably fall out of this without any miracle required, since it is right there in the soup next to its own RNA and can keep making lots of DNAs over and over. And so then
9) with reverse transcriptase floating about, converting randomly-generated RNAs into DNAs which themselves transcribe into RNAs, the soup now has a bunch of random RNA/DNA strings undergoing replication, along with a lot of replication engines and replication systems for the replication engine itself. So
10) then Darwin's logic applies: More replicatable stuff that randomly occurs, that happens to work better at being around for replication, and that therefore survives longer in the environment of replicating engines, will happen to get replicated more, and thus there will be a drift towards adaptive and useful parts, and to their combination in adaptive and useful ways, since those parts and combinations happen to be around longer and thus are present for replication more and therefore are replicated more often and therefore come to be more common.
So that is my idea of the essence of the evolution of life. There apparently were greasy puddles of nucleotides in the right part of the planet's evolution, undergoing day/night heat cycling and able to do protein synthesis without further aids. So with the one miracle of the random coming-together of the RNA for reverse transcriptase, the rest seems to be just cool and wonderful, but not actually dependent on God to overcome the infinite improbability of it all.

RNA, HIV, and the Origins of Life

http://www.science20.com/evolutionary_economics/blog/rna_hiv_and_origins_life

The central dogma of Molecular Genetics is that information flow is unidirectional:  DNA to RNA to PROTEIN.  That is, DNA holds the blueprints, RNA is the messenger, and Proteins are the constructed functional units of life.

This dogma seems to hold for most of the species on the planet.  From bacteria to humans to insects, the central dogma acts as a unifying theory of life’s architecture.   But, there are a few key exceptions.

The first is that in some viruses, there is no DNA at all!  Instead, they used RNA exclusively for their coding.  Among these are the viruses that cause the common cold, flu, polio, and hepatitis.  In these, the flow of information is simply:  RNA to PROTEIN.

Another remarkable exception to the central dogma is that of retroviruses.  These break a big rule!  (Namely, that flow of information is unidirectional.)  A retrovirus is so called because it, like the above viruses begins with RNA, but it is able (by way of an enzyme called, appropriately, “reverse transcriptase”) to catalyze the formation of DNA from its RNA molecule.  The flow of information is then:  RNA to DNA to RNA to PROTEIN.   HIV is an example of a retrovirus.  It gets into the cell, creates new DNA that then incorporates itself into the hosts chromosome and gets nasty.

Why is this important to the discussion about evolution and life’s origins?  Because it is highly unlikely that life began with DNA.  DNA is far too complex, secure, and doesn’t have the enzymatic properties of RNA.  DNA is double stranded where RNA is single stranded.  This makes RNA more able to react chemically with other molecules in the environment.

In spite of how remarkably important it is to life on the planet today, DNA at one time didn’t exist.  But, that doesn’t mean life didn’t exist.  The first complex organisms may have been RNA carrying viruses.

Could a retrovirus be responsible for creating the first DNA carrying organism?  I dunno, but it’s an interesting question.

Is it justified to blame God for creating pathogenic Coronaviruses ?
 
With the recent outbreak of the Coronavirus, some might ask: Why did God create pathogenic viruses? Does that substantiate the accusation ( so often heard, coming from the atheist camp) that God cannot be benevolent, but is evil?

Coronavirus lineages suggest that bat coronaviruses are older than those recognized in other animals and that the human severe acute respiratory syndrome from coronavirus was directly derived from viruses from wild animals in wet markets of southern China. Bats are likely the natural hosts for all presently known coronavirus lineages and that all coronaviruses recognized in other species were derived from viruses residing in bats. 11

Coronaviruses cause respiratory and intestinal infections in animals and humans1. They were not considered to be highly pathogenic to humans until the outbreak of severe acute respiratory syndrome (SARS) in 2002 and 2003 in Guangdong province, China 3

Remarkably, in Leviticus 11.13, we read:
13 “‘These are the birds you are to regard as unclean and not eat because they are unclean:....... and the bat.

The 21 viral types that wreak havoc with the human body represent an insignificant fraction of the 100 million viral types on earth. Most viruses are actually vital to our very existence. They keep ecosystems diverse and balanced.
Bacterial death is absolutely necessary for other living organisms.

Our mismanagement did put us at risk of some viruses. So we don’t know where Ebola comes from, but if we knew where it came from, would we be able to link it to mismanagement or just ignorance? We’ve encountered viruses in places where we went for pretty ecologically destructive reasons. Those viruses passing into humans and causing disease resulted from mismanagement coupled with not knowing.10

Globally the oceans contain 10^30 viruses. If you lined them all up they would extend for 10 million light-years or 100 times the distance across our galaxy. Collectively they would weigh as much as 75 million blue whales. Viruses are not living organisms. They are simply bits of genetic material (DNA or RNA) covered in protein, that behave like parasites. They attach to their target cell (the host), inject their genetic material, and replicate themselves using the host cells’ metabolic pathways.

Algae and plants are primary producers, the foundation of the world’s ecosystems. Using sunlight they turn raw elements like carbon dioxide, nitrogen, and phosphorus into organic matter. In turn, they are eaten by herbivores, which are in turn eaten by other animals, and so on. Energy and nutrients are passed on up the food chain until animals die. But what ensures that the primary producers get the raw elements they need to get started?

The answer hinges on the viruses’ relationship with bacteria. A virus doesn’t go hunting for its prey. It relies on randomly encountering a host — it’s a numbers game. When the host, such as a bacterial cell, grows rapidly, that number increases. The more of a bacterial species there is, the more likely it will come into contact with its viral nemesis — “killing the winner”. This means that no single bacterial species dominates an ecosystem for very long.

In freshwater, for example, you see very high rates of bacterial growth. You would think this high bacterial production would become part of the food chain and end up as fish food. But that is rarely the case.

We now realize that the bacteria actually disappear from these ecosystems. So where do the bacteria go?

The answer lies in the interaction of bacteria and viruses. When a virus bursts open a bacterial cell its “guts” are spewed back into the water along with all the new viruses. The cell contents then become food for the neighboring bacteria, thereby stimulating their growth. These bacteria increase in numbers and upon coming into contact with their viral nemesis they, too, become infected and lyse. This process of viral infection, lysis, and nutrient release occur over and over again. Bacteria are, in effect, cannibalizing each other with the help of their associated viruses. Very quickly, the elements that support the food web are put back into circulation with the help of viruses.

This interaction ensures inorganic nutrients are readily available to algae and plants on which ecosystems depend. It’s the combination of high bacterial growth and viral infection that keeps ecosystems functioning.  Freshwater viral/bacterial interactions appear to be a critical link in carbon cycle between the land and atmosphere. 9

The Logic of Chance: The Nature and Origin of Biological Evolution, Eugene V. Koonin:
Probably an even more fundamental departure from the three-domain schema is the discovery of the Virus World, with its unanticipated, astonishing expanse and the equally surprising evolutionary connectedness. Virus-like parasites inevitably emerge in any replicator systems, so THERE IS NO EXAGGERATION IN THE STATEMENT THAT THERE IS NO LIFE WITHOUT VIRUSES.

The role of viruses in ecology
Viruses are important microbial predators that influence global biogeochemical cycles 8  They are not primarily pathogens, which is a biased view based on the history of medicine. Most viruses do not cause diseases. Viruses cause diseases if a well-established equilibrium gets out of balance. Viruses help in building genomes. Viruses and bacteria belong to the human body and our environment as a well-balanced ecosystem. Only in unbalanced situations do viruses cause infectious diseases or cancer. 7  Although bacteria pass genetic information to each other using several processes such as pili transfer (see below), viral transfer is now known to be critically important. Viruses normally do not, and should not, cause disease. Only if something goes wrong, such as a mutation or accidental inappropriate movement of genes, do they cause problems. Evidence is accumulating to suggest that most or all harmful viruses and bacteria are mutated forms of non-pathogens. Pathogenic organisms result from gene shuffling, which inadvertently disrupts the normal species-host relationship. 6  

In this world of fast and easy travel, emerging viruses are increasingly becoming a major danger to world health. Coronaviruses are a notable example. Particularly virulent forms have emerged from their natural animal hosts and pose a threat to human communities. 2

Coronaviruses

Coronaviruses contain a genome composed of a long RNA strand—one of the largest of all RNA viruses. This genome acts just like a messenger RNA when it infects a cell, and directs the synthesis of two long polyproteins that include the machinery that the virus needs to replicate new viruses. These proteins include a replication/transcription complex that makes more RNA, several structural proteins that construct new virions, and two proteases. The proteases play essential roles in cutting the polyproteins into all of these functional pieces.

Proteases likely arose at the earliest stages as destructive enzymes necessary for protein catabolism and the generation of amino acids in primitive organisms. 2  Proteases act as sharp scissors and catalyze highly specific reactions of proteolytic processing, producing new protein products. They are relevant in the control of multiple biological processes in all living organisms. Proteases regulate the fate, localization, and activity of many proteins, modulate protein-protein interactions, create new bioactive molecules, contribute to the processing of cellular information, and generate, transduce, and amplify molecular signals.

As a direct result of these multiple actions, proteases influence DNA replication and transcription, cell proliferation and differentiation, tissue morphogenesis and remodeling, heat shock and unfolded protein responses, angiogenesis, neurogenesis, ovulation, fertilization, wound repair, stem cell mobilization, hemostasis, blood coagulation, inflammation, immunity, autophagy, senescence, necrosis, and apoptosis.

Consistent with these essential roles of proteases in cell behavior and survival and death of all organisms, alterations in proteolytic systems underlie multiple pathological conditions such as cancer, neurodegenerative disorders, and inflammatory and cardiovascular diseases.

Proteases also play key roles in plants and contribute to the processing, maturation, or destruction of specific sets of proteins in response to developmental cues or to variations in environmental conditions.

The main protease of coronavirus makes most of these cuts. The one shown (PDB entry 6lu7) is from the 2019-nCoV coronavirus that is currently posing dangers in Wuhan. It is a dimer of two identical subunits that together form two active sites.

1. https://www.hpcwire.com/off-the-wire/protein-data-bank-archive-adds-new-coronavirus-protease-structure/
2. https://pdb101.rcsb.org/motm/242
3. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/30531947
4. https://www.rcsb.org/3d-view/6LU7/1
5. https://en.wikipedia.org/wiki/Coronavirus
6. https://creation.com/did-god-make-pathogenic-viruses
7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755228/
8. https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2009.02101.x
9. https://theconversation.com/viruses-dont-deserve-their-bad-rap-theyre-the-unsung-heroes-you-never-see-46887
10. https://www.christianitytoday.com/ct/2018/august-web-only/why-zika-and-other-viruses-dont-disprove-gods-goodness.html
11. https://jvi.asm.org/content/81/8/4012

Cells could not have evolved without viruses

Cells could not have evolved without viruses, as they need reverse transcriptase (which is found only in viruses) in order to move from RNA to DNA.

In other words, instead of helping to solve the problem of the origin of life on Earth, recent research has only served to highlight one of its central paradoxes. And yet the science media reports the latest discoveries as if the solution is just around the corner. Don’t you find that just a little strange?

Globally the oceans contain 10^30 viruses. If you lined them all up they would extend for 10 million light-years or 100 times the distance across our galaxy. Collectively they would weigh as much as 75 million blue whales. Viruses are not living organisms. They are simply bits of genetic material (DNA or RNA) covered in protein, that behave like parasites. They attach to their target cell (the host), inject their genetic material, and replicate themselves using the host cells’ metabolic pathways.

Algae and plants are primary producers, the foundation of the world’s ecosystems. Using sunlight they turn raw elements like carbon dioxide, nitrogen, and phosphorus into organic matter. In turn, they are eaten by herbivores, which are in turn eaten by other animals, and so on. Energy and nutrients are passed on up the food chain until animals die. But what ensures that the primary producers get the raw elements they need to get started?

The answer hinges on the viruses’ relationship with bacteria. A virus doesn’t go hunting for its prey. It relies on randomly encountering a host — it’s a numbers game. When the host, such as a bacterial cell, grows rapidly, that number increases. The more of a bacterial species there is, the more likely it will come into contact with its viral nemesis — “killing the winner”. This means that no single bacterial species dominates an ecosystem for very long.

In freshwater, for example, you see very high rates of bacterial growth. You would think this high bacterial production would become part of the food chain and end up as fish food. But that is rarely the case.

We now realize that the bacteria actually disappear from these ecosystems. So where do the bacteria go?

The answer lies in the interaction of bacteria and viruses. When a virus bursts open a bacterial cell its “guts” are spewed back into the water along with all the new viruses. The cell contents then become food for the neighboring bacteria, thereby stimulating their growth. These bacteria increase in numbers and upon coming into contact with their viral nemesis they, too, become infected and lyse. This process of viral infection, lysis, and nutrient release occur over and over again. Bacteria are, in effect, cannibalizing each other with the help of their associated viruses. Very quickly, the elements that support the food web are put back into circulation with the help of viruses.

This interaction ensures inorganic nutrients are readily available to algae and plants on which ecosystems depend. It’s the combination of high bacterial growth and viral infection that keeps ecosystems functioning.  Freshwater viral/bacterial interactions appear to be a critical link in carbon cycle between the land and atmosphere. 9

Viruses are important microbial predators that influence global biogeochemical cycles 8They are not primarily pathogens, which is a biased view based on the history of medicine. Most viruses do not cause diseases. Viruses cause diseases if a well-established equilibrium gets out of balance. Viruses help in building genomes. Viruses and bacteria belong to the human body and our environment as a well-balanced ecosystem. Only in unbalanced situations do viruses cause infectious diseases or cancer. 7  Although bacteria pass genetic information to each other using several processes such as pili transfer (see below), viral transfer is now known to be critically important. Viruses normally do not, and should not, cause disease. Only if something goes wrong, such as a mutation or accidental inappropriate movement of genes, do they cause problems. Evidence is accumulating to suggest that most or all harmful viruses and bacteria are mutated forms of non-pathogens. Pathogenic organisms result from gene shuffling, which inadvertently disrupts the normal species-host relationship. 6  

In this world of fast and easy travel, emerging viruses are increasingly becoming a major danger to world health. Coronaviruses are a notable example. Particularly virulent forms have emerged from their natural animal hosts and pose a threat to human communities. 2

Viruses contain a genome composed of  RNA strands. Their Genomes acts just like a messenger RNA when it infects a cell and directs the synthesis of two long polyproteins that include the machinery that the virus needs to replicate new viruses. These proteins include a replication/transcription complex that makes more RNA, several structural proteins that construct new virions, and two proteases. The proteases play essential roles in cutting the polyproteins into all of these functional pieces.

Proteases likely arose at the earliest stages as destructive enzymes necessary for protein catabolism and the generation of amino acids in primitive organisms. 2  Proteases act as sharp scissors and catalyze highly specific reactions of proteolytic processing, producing new protein products. They are relevant in the control of multiple biological processes in all living organisms. Proteases regulate the fate, localization, and activity of many proteins, modulate protein-protein interactions, create new bioactive molecules, contribute to the processing of cellular information, and generate, transduce, and amplify molecular signals.

As a direct result of these multiple actions, proteases influence DNA replication and transcription, cell proliferation and differentiation, tissue morphogenesis and remodeling, heat shock and unfolded protein responses, angiogenesis, neurogenesis, ovulation, fertilization, wound repair, stem cell mobilization, hemostasis, blood coagulation, inflammation, immunity, autophagy, senescence, necrosis, and apoptosis.

Consistent with these essential roles of proteases in cell behavior and survival and death of all organisms, alterations in proteolytic systems underlie multiple pathological conditions such as cancer, neurodegenerative disorders, and inflammatory and cardiovascular diseases.

Proteases also play key roles in plants and contribute to the processing, maturation, or destruction of specific sets of proteins in response to developmental cues or to variations in environmental conditions.

The main protease of coronavirus makes most of these cuts. The one shown (PDB entry 6lu7) is from the 2019-nCoV coronavirus that is currently posing dangers in Wuhan. It is a dimer of two identical subunits that together form two active sites.

1. https://www.hpcwire.com/off-the-wire/protein-data-bank-archive-adds-new-coronavirus-protease-structure/
2. https://pdb101.rcsb.org/motm/242
3. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/30531947
4. https://www.rcsb.org/3d-view/6LU7/1
5. https://en.wikipedia.org/wiki/Coronavirus
6. https://creation.com/did-god-make-pathogenic-viruses
7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755228/
8. https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2009.02101.x
9. https://theconversation.com/viruses-dont-deserve-their-bad-rap-theyre-the-unsung-heroes-you-never-see-46887
10. https://www.christianitytoday.com/ct/2018/august-web-only/why-zika-and-other-viruses-dont-disprove-gods-goodness.html
11. https://jvi.asm.org/content/81/8/4012

Why Is Abiogenesis Impossible?

Many bacteria and all viruses possess less complexity than required for an organism normally defined as “living,” and for this reason must live as parasites that require the existence of complex cells in order to reproduce. For this reason, Trefil noted that the question of where viruses come from is an “enduring mystery” in evolution. Viruses usually are much smaller than parasitic bacteria and are not considered alive because they must rely on their host even more than bacteria do. Viruses consist primarily of a coat of proteins surrounding DNA or RNA that contains a handful of genes, and since they do not reproduce in the normal way, it's hard to see how they could have gotten started. One theory: they are parasites who, over a long period of time, have lost the ability to reproduce independently… Viruses are among the smallest of “living” things. A typical virus, like the one that causes ordinary influenza, may be no more than a thousand atoms across. This is in comparison with cells which may be hundreds or even thousands of times that size. Its small size is one reason that it is so easy for a virus to spread from one host to another--its hard to filter out anything that small (Trefil, 1992, p. 91).

In order to reproduce, a virus's genes must invade a living cell and take control of its much larger DNA. A bacterium is 400 times greater in size than the smallest known virus, while a typical human cell averages 200 times larger than the smallest known bacterium. The QB virus is only 24 nanometers long, contains only 3 genes and is almost 20 times smaller than Escherichia coli, billions of which inhabit the human intestines. E. coli is 1,000 nanometers long compared to a typical human cell that is about 10,000 nanometers long (1 nanometer equals 1 billionth of a meter, or about 1/25-millionths of an inch) and contains an estimated 100,000 genes. Researchers have detected microbes in human and bovine blood that are only 2-millionths of an inch in diameter, but these organisms cannot live on their own because they need more than simple inorganic, or common inorganic molecules to survive.

Since parasites lack many of the genes (and other biological machinery) required to survive on their own, in order to grow and reproduce they must obtain the nutrients and other services they require from the organisms that serve as their hosts. Independent free-living creatures such as people, mice and roses are far more complex than organisms like parasites and viruses that are dependent on these complex free-living organisms. Abiogenesis theory requires that the first life forms consisted of free-living autotrophs (i.e. organisms that are able to manufacture their own food) since the complex life forms needed to sustain heterotrophs (organisms that cannot manufacture their own food) did not exist until later.

The simplest microorganisms, Chlamydia and Rickettsea, are the smallest living things known, but also are both parasites and thus too simple to be the first life. Only a few hundred atoms across, they are smaller than the largest virus and have about half as much DNA as do other species of bacteria. Although they are about as small as possible and still be living, these two forms of life still possess the millions of atomic parts necessary to carry out the biochemical functions required for life, yet they still are too simple to live on their own and thus must use the cellular machinery of a host in order to live (Trefil, 1992, p. 28). Many of the smaller bacteria are not free-living but are parasite-like viruses that can live only with the help of more complex organisms (Galtier et al., 1999).

The gap between non-life and the simplest cell is illustrated by what is believed to be the organism with the smallest known genome of any free living organism Mycoplasma genitalium (Fraser et al., 1995). M. genitalium is 200 nanometers long and contains only 482 genes or over 0.5 million base pairs which compares to 4,253 genes for E. coli (about 4,720,000 nucleotide base pairs), with each gene producing an enormously complex protein machine (Fraser et al., 1995). M. genitalium also must live off other life because they are too simple to live on their own. They invade reproductive tract cells and live as parasites on organelles that are far larger and more complicated but which must first exist for the survival of parasitic organisms to be possible.

http://christiananswers.net/q-crs/abiogenesis.html

http://www.trueorigin.org/abio.php

Trefil noted that the question of where viruses come from is an “enduring mystery” in evolution.