The Mystery of Life on Earth and Origin of the Corona Virus

lim ju boo

Date:  May 28, 2020

The blogger’s note:

I am most honoured to be entrusted by the Great Sifu Dr. Lim Ju Boo to publish the following essay which according to him took him 3 days and 2 nights to write. Enjoy reading!

The Author’s note:

Before reading, kindly click either to one of the violin music sites or all three sequentially below to accompany your reading.

Use a home computer with good speakers than using smart phones.

1. https://www.youtube.com/watch?v=YmDNhi07_Ho 

2. https://www.youtube.com/watch?v=i3QGdJJZCSI 

3. https://www.youtube.com/watch?v=oegdYnak0-c

Listening in pensive mood is far more relaxing that way.

Thank you. Have a nice read!

A Private Communication:

A medical specialist friend whom I know since our student’s days at the university called me over the phone last evening for my opinion on the origin of the corona virus that is currently causing a pandemic outbreak.

He asked if this virus could have been artificially created, and if not, if I could enlighten the scientific world especially the virologists and the public its origin as he told me there are currently too many confusing claims, theories and conspiracies been circulated over the social media.

I was quite surprised at his question as I am just as doubtful and unclear as many others on its origin.

But I am sure it was not artificially created at the Wuhan Institute of Virology in China or anywhere else in the world. Neither was it spontaneously generated by bats nor the pangolins as its origin is unknown. 

Furthermore bats or any living organisms can only produce its own body cells and its own kind through reproduction, and definitely no animal can generate or produce a virus out of its own body.

If it was merely carried or transmitted by bats then there must have an origin somewhere. Unfortunately we have no record or clue to its evolutionary origin or history.

However, as someone familiar with the subject on the evolution of life on Planet Earth, I may be able to very briefly explain how all life including viruses may have started.

Here’s the scenario on how all life may have started and flourished on Earth very briefly explained with random samples taken in the timeline over the billions of years.

Earliest Life:

Evolutionary biologists believe the first pre-life started around 4,000 million years ago when what we call was the beginning of prebiotic chemistry.

Then about 200 million years later (3,800 million years ago), the first chemical fossils - the RNA world began to emerge.

It was in this period that all life forms began as a virus through random chance of synthesis of nitrogen compounds and sugars floating in the warm primordial oceans to generate the first RNA molecule from which all viruses constitute their genomic make-up. But it took a very long time for this random chance to occur. That period may have taken 743 million years after earth was created 4.543 billion years ago.

The accretion of earth took place between 4.5 to 4.4 billion (4,500 – 4,400 million) years ago when the Universe was created from the Big Bang. That was around 13.8 billion years ago.

The first DNA and protein life started only in 36,000 million years ago and the first photosynthesis (autotrophy) began 3,500 million years ago when Archaea and bacteria split.

The oldest large organism only surfaced in 575 million years ago, and the first insects emerged 396 million years ago, with the insects being one of the most successful that flourished in tremendous abundance and species

Earliest Fossils:

Scientists make use of preserved remnants of living creatures left behind called fossils to make a study and draw conclusions.

Among the earliest known fossils were the cnidarians, the group sea creatures that include jellyfish, sea anemones and corals, which were dated to around 580 million years ago though the fossil evidence has been disputed.

Then 5 million years later (575 million years ago), strange life forms known as the Ediacarans began to appear and this persisted for about 33 million years.

Then another 5 million years later (570 million years ago) there was a genetic drift when a small group known as the Ambulacraria breaks away from the main group of deuterostomes.

This group eventually became the echinoderms consisting of starfish, brittle stars and their relatives, and two worm-like families called the hemichordates and Xenoturbellida also began to emerge.

Then emerged the sea lily, another echinoderm thought to be the “missing link”between vertebrates (animals with backbones) and invertebrates (animals without backbones). The sea lily came in between around this time.

But fossilized animals appeared only about 565 million years ago.

Around 540 million years ago the first chordates – animals that have a backbone or at least a primitive version of it surfaced among the deuterostomes.

Then arose the sea squirts (tunicates) that began their lives as tadpole-like chordates, but metamorphosed part of their lives as bottom-dwelling filter feeders somewhat like a bag fastened to a rock.

Their larvae still looked like tadpoles today, somewhat suggesting their close relationship with backboned animals.

The Cambrian Explosion:

Then suddenly there was an explosion of various forms of life on Earth like myriads of flowers blooming in the fields in Spring.

The Cambrian Explosion, also called Cambrian Radiation happened around 535 million years ago, but we are unsure why this explosion of life unexpectedly occurred? One reason we think is our inability to find older fossils which may have occurred earlier.

But it was not until 530 million years ago that the first true vertebrate (an animal with a backbone) emerged. It probably evolved from a jawless fish that has a notochord, a stiff rod of cartilage, instead of a true backbone.

The first vertebrate is believed to look probably quite like a lamprey, hagfish or lancelet. Around the same time, the first clear fossils of trilobites surfaced. 

These are invertebrates similar in appearance to gigantic woodlice that grew up to 70 centimeters in length.

These creatures mushroomed in numbers in the oceans for the next 200 million years.

The next scenario 10 million years later (520 million years ago) was the appearance of Conodonts as another early form of vertebrate. They probably look like eels.

Cambrian Life was confined mainly to the sea, but there is some evidence the first steps onto land were taken by the end of this Period since the Cambrian Radiation was between 542 – 488 million years ago.

The Evolution of Fish:

Marine life like the evolution of fish began about 530 million years ago during the Cambrian explosion. It was during this time that the early chordates developed the skull and the vertebral column, leading to the first craniates and vertebrates.

The first fish lineages belong to the Agnatha, or jawless fish. Early examples include Haikouichthys.

During the late Cambrian, eel-like jawless fish called the conodonts (chordates resembling eels), and small mostly armoured fish known as ostracoderms, made their first appearances.

Most jawless fish are now extinct; but the extant lampreys may approximate ancient pre-jawed fish.

The oldest fossils found are around 3.48 billion years old (2)(3)(4).

Since most of the early lives arose from the seas it would be easier to investigate how fish and shellfish and marine life rose from the ancient waters

All that needs to be done is to catch ancient fish living in deep waters, or shellfish such as bivalves in shallow waters by merely collecting them from seashores or from reefs, and analyzing them in a laboratory.

Alternatively barnacles may be used to look at the evolutionary history. 

A barnacle is a type of arthropod constituting the infraclass Cirripedia in the subphylum Crustacea, and is hence related to crabs and lobsters. Barnacles are exclusively marine, and tend to live in shallow and tidal waters, and hence easier to capture and collect for study.

These specimens once collected can be preserved in suitable preservatives such as in saturated salt solutions, in formalin or in alcohol and sent to a laboratory for analysis. Such studies includes histology and microscopy which we shall briefly discuss later.

The Dinosaurs:

Millions of years later only did land animals such as dinosaurs emerge. We shall use the dinosaurs as an example to represent life in pre-historic eras partly because they go between the reptiles and the warm-blooded birds and partly because the dinosaurs are very late comers and are far easier to study from the fossil bones they left behind, as well as they are the ones most studied in evolutionary history.

Dinosaurs are a diverse group of reptiles called the Dinosauria.

They first emerged during the Triassic period between 243 and 233.23 million years ago, though the exact origin and timing of their appearance is still being investigated.

They grew into the prevailing terrestrial vertebrates after the Triassic–Jurassic extinction an event around 201.3 million years ago, and their supremacy remained throughout the Jurassic and Cretaceous periods.

Their fossil records suggest that birds are modern feathered dinosaurs, having evolved during the Late Jurassic epoch.

They went extinct about 65 million years ago at the end of the Cretaceous Period, after roaming the Earth for about 165 million years.

After the dinosaurs disappeared, birds as we know them today began to appear and they were the only dinosaur lineage to survive the Cretaceous–Paleogene extinction event which took place approximately 65 - 66 million years ago.

I remember when I was an undergraduate student in zoology between 1961 – 1964 (among many other entirely different types of courses such as chemistry, physiology, nutrition, food quality control, microbiology, biomedical sciences and medicine I studied later), one of our senior lecturers in zoology told us birds are glorified reptiles as the dinosaurs were also reptiles.

That was quite a surprising statement to me then since even in those years I knew that reptiles were cold-blooded and sluggish, whereas birds are endothermic (warm-blooded) animals, and maintaining endothermy is costly for the birds as they use up no less than 90% of total metabolism just to maintain their higher body temperature than all mammals.

Their body temperatures are between 37.7 to 43.5֩°C, compared to those of mammals whose body temperatures are between 36 - 39°C. This is part of their metabolic adaptation during their evolution since they need to take flight often over very long distances across oceans and seas almost non-stop especially during their migratory periods to warmer climates.

Hence they need to be very active with extremely high metabolic rates, compared to cold-blooded reptiles.

But evolutionary biologists now have gathered sufficient evidences to show that birds are not just gloried reptiles but gloried dinosaurs.

    

However from the evolutionary biology point-of-view, dinosaurs can again be divided into avian dinosaurs which are birds, and non-avian dinosaurs, which are all dinosaurs other than birds.

Dinosaurs as Birds:

There are over 10,000 living species of birds, and they are the most diverse group of vertebrates besides perciform fish.

Paleontologists have identified there are over 500 distinct genera and more than 1,000 different species of non-avian dinosaurs in evolutionary history.

Dinosaurs are represented on every continent by both surviving species of birds, and the rest from fossil remains.

But before birds were recognized as dinosaurs and glorified reptiles, scientists once thought dinosaurs were cold-blooded.

However most of the studies conducted since the 1970's, found that all dinosaurs were actually active animals with warm metabolisms and several adaptations for social interactions.

Demise of the Dinosaurs:

Dinosaurs first made their appearance about 225 million years ago, during the Triassic period, and the last non-avian dinosaurs went extinct 65 million years ago.

Many theories have been proposed towards this mystery ranging from some kind of cataclysmic event like an asteroid impacts, volcanic eruptions, or both.

One of the best well-known theories for the demise of the dinosaurs is the Alvarez hypothesis, named after the father-and-son duo Luis and Walter Alvarez.

In 1980, these two father-son scientists proposed a hypothesis that a meteor the size of a mountain slammed into Earth 66 million years ago, filling the atmosphere with gas, dust, and debris that drastically cutting off sunlight, altered the climate and reducing food supply by cutting off photosynthesis.

The key evidence to their theory was that an unusually high amount of the metal iridium was found in the Cretaceous-Paleogene, or K-Pg, layer which is the geological boundary zone that seems to cap any known rock layers containing dinosaur fossils.

Iridium is relatively rare in Earth's crust but is more abundant in stony meteorites, which led the Alvarezs to conclude that the mass extinction was caused by an extraterrestrial object.

But scientists like Manabu Sakamoto from the University of Reading (one of my alma maters) and those from the University of Bristol have other theories.

Using statistical analysis, they concluded that for 50 million years before even the extinction of the dinosaurs, many other species were already going out of extinction faster than new ones were emerging for reasons unknown.

But let us not dwell into all these different theories on their disappearance mysteries.

Herbivorous and Carnivorous:

Some dinosaurs were herbivorous, others carnivorous. There were also evidences to propose that dinosaurs like birds were egg-laying, and that they built nests too, a common denominator shared by both avian and non-avian dinosaurs. This is some very surprising findings in the life history of these creatures.

All these findings among many, many more were part of the various investigations done in evolutionary biology.

Actually the evolution of life on Earth has a very long time line. Dinosaurs came long after the Cambrian explosion or Cambrian radiation (1).

It was a pre-dinosaurs event approximately 541 million years ago during the Cambrian period when practically all major animal phyla started appearing in the fossil record.

It lasted for about 13 million years (7)(8)(9) to 25 million years (10) (11), and resulted in the divergence of most modern metazoan phyla.(12) (13) (14) (15).

The question people puzzlingly ask is, how do scientists and evolutionary biological experts know all these scenarios took place billions of years ago?

The only way is to collect fossil remains for laboratory analysis. Let’s briefly have a look.

Laboratory Studies:

The most important method in the study how life evolved on Earth is to collect samples of dead and living specimens in the field for study.

Normally preserved remnants in the form of either trace, tell-tale signs or impressions of any ancient living creatures or of  life  called  fossils, that represents some ancient living creatures from a past geological age are collected for study in a laboratory.

These could be bones, shells, exoskeletons, stone imprints of animals or microbes, objects preserved in amber, hair, petrified wood, oil, coal, and even remnants of DNA. These collective remnants are known as the fossil record.

Paleontology is the study of fossils: their age, method of formation, and evolutionary significance. Specimens are usually considered to be fossils if they are over 10,000 years old. (1). How are they investigated?

Morphology and Histology:

Morphology gives a general description and gross description and the anatomy of the sample. This examination is first done before dissecting them.

Histology is the study of the microscopic anatomy of cells, tissues, and organs as seen through a microscope. It examines the correlation between structure and function.

Normally this entails dissecting the collected samples, embedding them in paraffin wax, and cutting them with a microtome. The tissues are then stained for study under a microscopy or even using other techniques of preparation for electron microscopy.

The most common technique used before histology is embedding the tissues in paraffin wax or plastic, then sectioning the block, mounting the thin slices on microscope slides, and staining them to help distinguish one type of tissue from another.

Histology allows evolutionary biologists to examine the inner structures of soft anatomy, or to reconstruct the anatomy of species that are too small to dissect by hand. Their structures may give clues how anatomical structures were evolved over the millions of years.

Sedimentary Rocks:

Another method to understand how ancient species were evolved is to use fossil evidence as already briefly discussed. Fossils are most often found in sedimentary rock.

Sediments are sand or clay which settled at the bottom of a body of water. Over a period of time, the layer of sediment is covered by overlapping new layers. As these layers becomes heavier, the sediment solidify into sedimentary rock.

Dead organisms can be concealed under new layers of sediment and or conserved in sedimentary rocks. This process can generate fossils.

Electron Microscopy:

Besides light-transmission microscopy, an electron microscope may also be used for sub-microscopic detailed studies.

Electron microscopy uses beams of electrons instead of light. This gives a much higher magnifications where a specimen is needed to provide a much more detailed information about a certain structure.

These high-energy electron beams examine and photograph further details on the shells and skeletons and anatomy or other parts of the specimen to examine their formation.

Scanning electron microscopy (SEM) provides high-resolution images of outside surfaces, like sculpture, a hinge, or the appearance of the siphons.

Transmission electron microscopy (TEM) provides very fine details of cross sections of tissues, such as sperm that are still under development, say in the specimen of reproductive tract under study.

Molecular Methods:

Another method used in the investigation is DNA or RNA isolation and their sequencing.

These are very valuable methods to determine evolutionary pathways and relationships among various species.

In some ways DNA and RNA analysis can be more useful than gross morphology, since DNA is less inclined to actions of external forces such as food, temperature, and the location in which the ancient specimens were found or collected.

Genomic Sequencing:

Next comes genomic analysis. The basic procedure in gene sequencing involves extracting the DNA / RNA from the preserved specimen and purifying them.

For instance we can extract bones, shell or muscle fibers, skin, hair from a fresh sample or one already preserved in alcohol or in other preservative.

Scientists then decides which area of the gene (DNA) that needs to be amplified by using Polymerase Chain Reaction (PCR).  

This technique makes extra copies of the desired gene, using chemical and heat cycles. The amplification produces sufficient of the gene DNA for the sequencing procedure.

A PCR thermocycler machine does sequencing using chemical and heat cycles to duplicate copies of the gene sequence.

The result is then read using a Gene Sequencer.

Some sequencer machines use a laser to read a fluorescent "tag" attached to the DNA fragments to produce a chromatogram.

The chromatogram shows coloured patterns which are distinct zones of separated pigments of unidentified DNA patterns.

There are four bases of a DNA molecule, and these will be color-coded for easy identification, such as red zone A (adenine), green T (thymine), black G (guanine), and blue C (cytosine).

The arrangements of these sequences are then compared with another sample with similar or matching close biological lineages in an evolution tree.

Likewise, unmatched sequencing bases may also show up for comparison since their genomic signatures may be used for further phylogenetic analyses.

Other Sequencing Techniques:

One method in use since 2005 is the capillary sequencing but this has been progressively displaced by high output sequencing technologies such as Illumina dye sequencing, pyrosequencing, and SMRT sequencing.

All of these technologies continue to employ the basic shotgun strategy, namely, parallelization and template generation via genome fragmentation.

Other technologies are emerging, including nanopore technology. Though nanopore sequencing technology is still being refined, its portability and potential capability of generating long reads are of relevance to whole-genome sequencing applications.

Phylogenetic Analysis:

This is an analytical method used to look at the hypothesis of correlations among species. This is done by coding the various states of homologous characters called cladistics.

Scientists use the anatomical traits and/or molecular sequences to determine a phylogeny.

Sequence of ancestors of a particular lineage or history of an organism's lineage through time can then be traced. This phylogeny is a hypothesis based on taxon or taxa.

In short, it is a method to determine heritable traits, such as DNA sequences or morphology between species.

Using this analysis, organism or group of organisms of the same class such as members of an order, a family, genus, or species under study can then be identified by their genomic characteristics and traits

Radiometric Dating:

Another method evolutionary biologists look at is the linages and the origin of a species by using radioactive isotope tagging, called radiometric dating. This procedure banks on radioactive isotopes to determine the age of a fossil in years.

Since radioactive isotopes present in the body decay at a steady rate, scientists then looks at the half-life of these isotopes.

The biologist takes into account the time for half of the radioactive isotopes in a sample to breakdown into nonradioactive isotopes. By knowing how much non-radioactive isotopes were left gives the investigator clues to the age of the fossil.

Carbon Dating:

One form of this analysis is called carbon dating. This technique is useful for fossils of living organisms as they contain radioactive carbon-14.

The disadvantage of carbon-14 dating is that carbon-14 has a comparatively short half-life on the evolutionary scale.

Hence it may only be useful for dating relatively later stage fossils remains that are no older than 60,000 years old.

Alternatively, longer life radioactive isotopes such as potassium-40 may be used to determine the age of older fossils.

The difficulty of using long-life isotopes is that they are found in rock, and not in fossils.

Even then, these long-life isotopes permit scientists to date layers of sedimentary rock within which the fossils are embedded. It all depends on what timeline and life forms we are searching.

All these were determined using various methods including molecular clock in which molecular differences are used to determine when two lineages of species diverged later in the timeline of evolution.

Read more: 

https://www.newscientist.com/article/dn17453-timeline-the-evolution-of-life/#ixzz6NU7vM5Bm

https://www.newscientist.com/article/dn17453-timeline-the-evolution-of-life/#ixzz6NU7blLAO

https://www.newscientist.com/article/dn17453-timeline-the-evolution-of-life/#ixzz6NU7E3Yv9

https://www.newscientist.com/article/dn17453-timeline-the-evolution-of-life/#ixzz6NU6Qha3S

Having very briefly described some of the analytical tools scientists use to determine a geological and biological time scale of Earth’s history, they can then classify the various eons, eras, and periods during which life evolved in order to rate of their emergence on Earth  

Summary:

Life on Earth has a very long history which took between 4.5 to 4.4 billion (4500 – 4400 million) years to emerge after the Universe was created from the Big Bang. That event took place around 13.8 billion years ago.

Its origin of life itself is still unclear to us. Many theories have been proposed, but none definitive.

The theory of evolution is based on many studies and observations by scientists like Charles Darwin from the University of Cambridge who went round the world in the HMS Beagle with Captain Robert FitzRoy on a journey that took them 5 years.

Darwin also went to the Galapagos Islands and observed the beaks sizes of finches which were a group of about 26 species of passerine birds.

They are well known for their remarkable diversity in beak forms and sizes and functions since these finches need to adapt to break open seeds of various sizes due to seasonal variations.

Darwin then published his world-renown theory of evolution “The Origin of the Species”. Some other studies on evolution were also conducted by Jean-Baptiste Lamarck a French naturalist. But we shall not go all the details.

In the study of evolution and mystery of life on Earth biologists make use of fossils together with histology, microscopy, isotope dating and phylogenetic analysis to look at differences between species and determine their evolutionary linkages.

Differences between two similar species that became separate species may be due to various environmental challenges causing them to adapt, separate and speciate differently.

This causes a genetic drift in biodiversity - either by what population geneticists called as a “founder effect”, or a“bottleneck effect”.

There are many other techniques that may also be used such as the use of mitochondrial DNA analysis and also comparative anatomy to trace human ancestry and identification, although human evolution is a separate subject that came last and very much later.

However none of the study techniques can be used to trace the origin of the corona virus that is plaguing the world today.

This is because in the thinking of this author this virus has never occurred in the past with no genomic records available for comparison.

Unfortunately my ignorant doctor friend asked me for the impossible. The closest link between the Covid-19 virus is those found during the emergence of SARS in 2003, MERS in 2012 all of which is believed to be the same group of corona viruses, but none provide sufficient data or evidence their origin except sharing the same genomic data.

Where did they come from has been hotly debated and unbelievable stories and theories being circulated in videos and written text in their tens of hundreds among other conspiracies including the virus being artificially created either in China or America.

We cannot match anything, be they non-living viruses or pre-life molecules or any organism that stands alone and has no previous records or evidence to compare. We will not go into those presumptions for discussions.

This is supposed to be a very brief and very simple account written in simple non-technical language for readers to understand how evolutionary biologists trace the evolution of life on Earth over the few billions of years taking random samples of eons, periods, eras on which various life forms appeared.

Hence we shall not go too much into all the timeline of biological evolution as from the very beginning this author has to account for its history to be written in less than a 6,000 words, else he has to write a comprehensive account on evolution in the form of a text book between 500 – 800 pages with data, graphs diagrams, and photographs all thrown in. We will not do that for easy reading. 

This Covid-19 virus as well as the SARS virus may have originated from outer space. For this separate theory, kindly refer their origin by this author here:

Is SARS Virus A Harbinger from Another World:

https://scientificlogic.blogspot.com/2020/05/is-sars-virus-harbinger-from-another.html 

Also on the mystery on Covid-19 here:

2020: The War of the Worlds: Earthlings vs. The Corona Virus. Who will Win?

https://taionn.blogspot.com/2020/05/2020-war-of-worlds-earthlings-vs-corona.html

Thank you for your valuable time and effort reading.

jb lim

(4,907 words: 25 pages) 

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