Leave a comment


Ally Fogg

“When things go wrong, go wrong with you, it hurts me too.”

It’s not often that you can find guidance on modern gender issues from traditional 1940s blues standards, but there has rarely been a more succinct illustration that women’s issues are men’s concern, and vice versa. Our lives and fortunes are interlinked and interdependent, on both personal and societal planes.

View original post 694 more words

The Origin of “Life”

Leave a comment

Reading about DNA/RNA.

With my definition of “life,”

“the organization of matter and energy resulting from a genetic sequence,”

I’m in a better position to theorize about how it began. 



Abiogenesis, the study of the origin of life.We can demonstrate the truth of evolution, but the origin of life is something else entirely. Or is it? Well, we can’t definitively say whether or not it’s something else entirely until we have a definition of “life.” This is where I come in. If we define “life” as “the organization of matter and energy resulting from a genetic sequence,” we can then have a better idea of what to look for, exactly. Often, when speaking to those who would like to see the testable, verifiable, TRUE theory of evolution de-legitimized, they make a leap between The Big Bang and current biological diversity. Or the apparent implausibility of life forming at all. Still, while both scientists and laypeople speak on these things, neither have anything beyond a vague impression or a laundry list of characteristics about what GENERALLY constitute life. I decided on a whim to just settle the question in my mind once and for all.  




This talk would define life as “evolvable matter.” This seems simple enough… but this harkens back to the “life as something that can reproduce: trope. Obviously, something is still alive even when it’s mechanism for reproduction has been removed, unless you’re playing with semantics. It’s important to establish that EVEN though some life form came about without a means of reproduction, what’s most pertanent is that we establish a context where such a thing could have come about at all. When we do, we’re also establishing a context where a reproducing life form could have come about as well.


With my definition in mind, I scurried the internet for a plausible narrative for the origin of life. This piece was written in real time, as I was reading the articles, watching the videos, and piecing it together sensibly.



Over the course of my study, I was struck my how much of the data that made abiogenesis plausible was discovered within the last decade.

Much like most of the data that makes evolution more plausible was discovered more recently. The previous generation had some wild-mass guessing to do, and it makes sense for them to settle with Hebrew Mythology in the face of the yawning chasms of unknowns linking theory and observable/testable facts. Thankfully we don’t live in that world anymore.


I did successfully construct a narrative for the plausibility of abiogenesis, and data supporting the possibility of its occurrence each step of the way. As I learn more, I will plug the new data in the correct sequence below. However, the bulk of what was written below was written and quoted at the time. 


For a simple, bullet point of the end results, you may scroll down to: IN SUMMARY…




Big things have small beginnings.

There is a great deal of molecular bonding involved in the composition of DNA, the more I read on it.

But… if one simple bacteria could form on its own… then we have liftoff.


Under what circumstances could such a thing happen, though? We can look up into the sky and observe the birth and death of stars, but we don’t have microscopic vision like Superman does.


To think… IF any bacteria formed on their own SINCE then, there’d be no way for us to know unless we knew when and where to look for such a thing.

We do not. And they’re probably liable to be picked off by the larger/more evolved cellular organisms in the microscopic ecosystem beyond our sight.


But presumable, the FIRST cells HAD no rivals. Until the first MUTATIONS happened, dividing the them irrevocably.


But it looks like THAT might have been a process too. Nothing spontaneous. Nothing unprecedented.

Biologists define “life” by listing characteristics we share/tend to share. They’ve got it backwards…


IF there was an environment where DNA/RNA strings could come about in random combinations… but didn’t have the tools to reproduce… many of the characteristics, but no reproduction. Or reproduction but nothing else… then death.


JUST an environment where these things can happen randomly…. ALL we need. Then we have the secret of the origin of life.

We’d have clinched it IF one of the spontaneous RNA/DNA sequences could self-replicate. Already done it?

Lincoln synthesized in the laboratory a large population of variants of the RNA enzyme that would be challenged to do the job, and carried out a test-tube evolution procedure to obtain those variants that were most adept at joining together pieces of RNA.

Ultimately, this process enabled the team to isolate an evolved version of the original enzyme that is a very efficient replicator, something that many research groups, including Joyce’s, had struggled for years to obtain. The improved enzyme fulfilled the primary goal of being able to undergo perpetual replication. “It kind of blew me away,” says Lincoln.


Immortalizing Molecular Information

The replicating system actually involves two enzymes, each composed of two subunits and each functioning as a catalyst that assembles the other. The replication process is cyclic, in that the first enzyme binds the two subunits that comprise the second enzyme and joins them to make a new copy of the second enzyme; while the second enzyme similarly binds and joins the two subunits that comprise the first enzyme. In this way the two enzymes assemble each other — what is termed cross-replication. To make the process proceed indefinitely requires only a small starting amount of the two enzymes and a steady supply of the subunits.


“This is the only case outside biology where molecular information has been immortalized,” says Joyce.

Not content to stop there, the researchers generated a variety of enzyme pairs with similar capabilities. They mixed 12 different cross-replicating pairs, together with all of their constituent subunits, and allowed them to compete in a molecular test of survival of the fittest. Most of the time the replicating enzymes would breed true, but on occasion an enzyme would make a mistake by binding one of the subunits from one of the other replicating enzymes. When such “mutations” occurred, the resulting recombinant enzymes also were capable of sustained replication, with the most fit replicators growing in number to dominate the mixture. “To me that’s actually the biggest result,” says Joyce.


The research shows that the system can sustain molecular information, a form of heritability, and give rise to variations of itself in a way akin to Darwinian evolution. So, says Lincoln, “What we have is non-living, but we’ve been able to show that it has some life-like properties, and that was extremely interesting.”

Joyce says that only when a system is developed in the lab that has the capability of evolving novel functions on its own can it be properly called life. “We’re knocking on that door,” he says, “But of course we haven’t achieved that.”

The subunits in the enzymes the team constructed each contain many nucleotides, so they are relatively complex and not something that would have been found floating in the primordial ooze. But, while the building blocks likely would have been simpler, the work does finally show that a simpler form of RNA-based life is at least possible, which should drive further research to explore the RNA World theory of life’s origins.



Depends on how you DEFINE “life,” geniuses…

It is a challenge for scientists and philosophers to define life in unequivocal terms.[19][20][21] This is difficult partly because life is a process, not a pure substance.[22] [23] Any definition must be sufficiently broad to encompass all life with which we are familiar, and must be sufficiently general to include life that may be fundamentally different from life on Earth. [24] [25] [26]


Since there is no unequivocal definition of life, the current understanding is descriptive. Life is considered a characteristic of organisms that exhibit all or most of the following:[25][27]

  1. Homeostasis: Regulation of the internal environment to maintain a constant state; for example, electrolyte concentration or sweating to reduce temperature.
  2. Organization: Being structurally composed of one or more cells — the basic units of life.
  3. Metabolism: Transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.
  4. Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter.
  5. Adaptation: The ability to change over time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism’s heredity, diet, and external factors.
  6. Response to stimuli: A response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion; for example, the leaves of a plant turning toward the sun (phototropism), and chemotaxis.
  7. Reproduction: The ability to produce new individual organisms, either asexually from a single parent organism, or sexually from two parent organisms.

These complex processes, called physiological functions, have underlying physical and chemical bases, as well as signaling and control mechanisms that are essential to maintaining life.



“The organization of matter and energy resulting from a genetic sequence.” -Me


As far as I’m concerned, it IS life… but we haven’t pinned down exactly how RNA first formed on its own, OR how RNA can turn to DNA… Or have we?

RNA, the single-stranded precursor to DNA, normally expands one nucleic base at a time, growing sequentially like a linked chain. The problem is that in the primordial world RNA molecules didn’t have enzymes to catalyze this reaction, and while RNA growth can proceed naturally, the rate would be so slow the RNA could never get more than a few pieces long (for as nucleic bases attach to one end, they can also drop off the other).


Ernesto Di Mauro and colleagues examined if there was some mechanism to overcome this thermodynamic barrier, by incubating short RNA fragments in water of different temperatures and pH.


They found that under favorable conditions (acidic environment and temperature lower than 70 degrees Celsius), pieces ranging from 10-24 in length could naturally fuse into larger fragments, generally within 14 hours.


The RNA fragments came together as double-stranded structures then joined at the ends. The fragments did not have to be the same size, but the efficiency of the reactions was dependent on fragment size (larger is better, though efficiency drops again after reaching around 100) and the similarity of the fragment sequences.




RNA and DNA are both nucleic acids, but differ in three main ways:

  • Unlike double-stranded DNA, RNA is a single-stranded molecule in many of its biological roles and has a much shorter chain of nucleotides.
  • While DNA contains deoxyribose, RNA contains ribose (in deoxyribose there is no hydroxyl group attached to the pentose ring in the 2′ position). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis.
  • The complementary base to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine.


DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds.



A phosphate, an inorganic chemical, is a salt of phosphoric acid.


Monosaccharides (from Greek monos: single, sacchar: sugar) are the most basic units of biologically important carbohydrates. They are the simplest form of sugar and are usually colorless, water-soluble, crystalline solids. Some monosaccharides have a sweet taste. Examples of monosaccharides include glucose (dextrose), fructose (levulose), galactose, xylose and ribose.


Now… onto the implications of potential formation of DNA from RNA…

Glimpses Of Earliest Forms Of Life On Earth: Remnant Of Ancient ‘RNA World’ Discovered

Breaker’s lab solved a decades-old mystery by describing how tiny circular RNA molecules called cyclic di-GMP are able to turn genes on and off. This process determines whether the bacterium swims or stays stationary, and whether it remains solitary or joins with other bacteria to form organic masses called biofilms. For example, in Vibrio cholerae, the bacterium that causes cholera, cyclic di-GMP turns off production of a protein the bacterium needs to attach to human intestines.


The tiny RNA molecule, comprised of only two nucleotides, activates a larger RNA structure called a riboswitch. Breaker’s lab discovered riboswitches in bacteria six years ago and has since shown that they can regulate a surprising amount of biological activity. Riboswitches, located within single strands of messenger RNA that transmit a copy of DNA’s genetic instructions, can independently “decide” which genes in the cell to activate, an ability once thought to rest exclusively with proteins.


Breaker had chemically created riboswitches in his own lab and – given their efficiency at regulating gene expressions – predicted such RNA structures would be found in nature. Since 2002, almost 20 classes of riboswitches, including the one described in today’s paper, have been discovered, mostly hidden in non-gene-coding regions on DNA.


“We predicted that there would be an ancient ‘RNA city’ out there in the jungle, and we went out and found it,” Breaker said.

Bacterial use of RNA to trigger major changes without the involvement of proteins resolves one of the questions about the origin of life: If proteins are needed to carry out life’s functions and DNA is needed to make proteins, how did DNA arise?


The answer is what Breaker and other researchers call the RNA World. They believe that billions of years ago, single strands of nucleotides that comprise RNA were the first forms of life and carried out some of the complicated cellular functions now done by proteins. The riboswitches are highly conserved in bacteria, illustrating their importance and ancient ancestry, Breaker said.



“RNA World,”  huh?

The RNA world hypothesis proposes that self-replicating ribonucleic acid (RNA) molecules were precursors to current life, which is based on deoxyribonucleic acid (DNA), RNA and proteins. RNA stores genetic information like DNA, and catalyzes chemical reactions like an enzyme protein. It may, therefore, have played a major step in the evolution of cellular life.[1]

The RNA world would have eventually been replaced by the DNA, RNA and protein world of today, likely through an intermediate stage of Ribonucleoprotein enzymes such as the ribosome and ribozymes, since proteins large enough to self-fold and have useful activities would only have come about after RNA was available to catalyze peptide ligation or amino acid polymerization.[2] DNA is thought to have taken over the role of data storage due to its increased stability, while proteins, through a greater variety of monomers (amino acids), replaced RNA’s role in specialized biocatalysis.

The RNA world hypothesis is supported by the observation that many of the most critical components of cells (those that evolve the slowest) are composed mostly or entirely of RNA. This would mean that the RNA in modern cells is an evolutionary remnant of the RNA world that preceded ours. Also, many critical cofactors (ATP, Acetyl-CoA, NADH, etc.) are either nucleotides or substances clearly related to them.



Okay, but what about the INITIAL formation of RNA/DNA?

“Molecular biologist’s dream”

“Molecular biologist’s dream” is a phrase coined by Gerald Joyce and Leslie Orgel to refer to the problem of emergence of self-replicating RNA molecules as any movement towards an RNA world on a properly modeled early Earth would have been continuously suppressed by destructive reactions.[44] It was noted that many of the steps needed for the nucleotides formation do not proceed efficiently in prebiotic conditions.[45]

Joyce and Orgel specifically referred the molecular biologist’s dream to “a magic catalyst” that could “convert the activated nucleotides to a random ensemble of polynucleotide sequences, a subset of which had the ability to replicate”.

Implications of the RNA world

The RNA world hypothesis, if true, has important implications for the definition of life. For most of the time that followed Watson and Crick’s elucidation of DNA structure in 1953, life was largely defined in terms of DNA and proteins: DNA and proteins seemed the dominant macromolecules in the living cell, with RNA only aiding in creating proteins from the DNA blueprint.

The RNA world hypothesis places RNA at center-stage when life originated. This has been accompanied by many studies[citation needed] in the last ten years that demonstrate important aspects of RNA function not previously known—and supports the idea of a critical role for RNA in the mechanisms of life.



Hrrm… Coming to a similar conclusion as I, it seems.

But about the RNA problem…?

One of the biggest problems in getting a polymer to form is that, as it grows, its two ends often react with each other instead of forming longer chains. The problem is known as strand cyclization, but Hud and his team discovered that using a molecule that binds between neighboring base pairs of DNA, known as an intercalator, can bring short pieces of DNA and RNA together in a manner that helps them create much longer molecules.

“If you have the intercalator present, you can get polymers. With no intercalator, it doesn’t work, it’s that simple,” said Hud.


Hud and his team also tested how much influence a midwife molecule might have had on creating DNA’s Watson-Crick base pairs (A pairs with T, and G pairs with C). They found that the midwife used could determine the base pairing structure of the polymers that formed. Ethidium was most helpful for forming polymers with Watson-Crick base pairs. Another molecule that they call aza3 made polymers in which each A base is paired with another A.


“In our experiment, we found that the midwife molecules present had a direct effect on the kind of base pairs that formed. We’re not saying that ethidium was the original midwife, but we’ve shown that the principle of a small molecule working as a midwife is sound. In our lab, we’re now searching for the identity of a molecule that could have helped make the first genetic polymers, a sort of ‘unselfish’ molecule that was not part of the first genetic polymers, but was critical to their formation,” said Hud.




A team led by Dr Paul Clarke in the Department of Chemistry at York has re-created a process which could have occurred in the prebiotic world.

Working with colleagues at the University of Nottingham, they have made the first step towards showing how simple sugars — threose and erythrose — developed. The research is published in Organic & Biomolecular Chemistry.

Dr Clarke said: “There are a lot of fundamental questions about the origins of life and many people think they are questions about biology. But for life to have evolved, you have to have a moment when non-living things become living — everything up to that point is chemistry.

“We are trying to understand the chemical origins of life. One of the interesting questions is where carbohydrates come from because they are the building blocks of DNA and RNA. What we have achieved is the first step on that pathway to show how simple sugars — threose and erythrose — originated. We generated these sugars from a very simple set of materials that most scientists believe were around at the time that life began.”



Carbs make you fat…

A carbohydrate is an organic compound that consists only of carbon, hydrogen, and oxygen, usually with a hydrogen:oxygen atom ratio of 2:1 (as in water); in other words, with the empirical formula Cm(H2O)n.

Formerly the name “carbohydrate” was used in chemistry for any compound with the formula Cm (H2O) n. Following this definition, some chemists considered formaldehyde (CH2O) to be the simplest carbohydrate,[3] while others claimed that title for glycolaldehyde.[4] Today the term is generally understood in the biochemistry sense, which excludes compounds with only one or two carbons.

Wait a minute…This reminds me…

Organic Carbon from Mars, but Not Biological


Steele’s team examined samples from 11 Martian meteorites whose ages span about 4.2 billion years of Martian history. They detected large carbon compounds in 10 of them. The molecules were found inside of grains of crystallized minerals.


Using an array of sophisticated research techniques, the team was able to show that at least some of the macromolecules of carbon were indigenous to the meteorites themselves and not contamination from Earth. Next the team looked at the carbon molecules in relation to other minerals in the meteorites to see what kinds of chemical processing these samples endured before arriving on Earth. The crystalline grains encasing the carbon compounds provided a window into how the carbon molecules were created. Their findings indicate that the carbon was created during volcanism on Mars and show that Mars has been doing organic chemistry for most of its history.


“These findings show that the storage of reduced carbon molecules on Mars occurred throughout the planet’s history and might have been similar to processes that occurred on the ancient Earth,” Steele said. “Understanding the genesis of these non-biological, carbon-containing macromolecules on Mars is crucial for developing future missions to detect evidence of life on our neighboring planet.”



What does “organic” mean in this context anyway?

An organic compound is any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of carbon-containing compounds such as carbides, carbonates, simple oxides of carbon (such as CO and CO2), and cyanides, as well as the allotropes of carbon such as diamond and graphite, are considered inorganic. The distinction between “organic” and “inorganic” carbon compounds, while “useful in organizing the vast subject of chemistry… is somewhat arbitrary”.



Arbitrary… definitions… AGAIN!? Hrrm… Whatever…Back to the formation of RNA…

The quest to recreate the chemistry that might have allowed life to emerge on a prehistoric Earth began in earnest in the 1950s. Since that time researchers have focused on a chemical path known as the formose reaction as a potential route from the simple, small molecules that might have been present on Earth before life began to the complex sugars essential to life, at least life as we know it now.


The formose reaction begins with formaldehyde, thought to be a plausible constituent of a prebiotic world, going through a series of chemical transformation leading to simple and then more complex sugars, including ribose, which is a key building block in DNA and RNA.


But as chemists continued to study the formose reaction they realized that the chemistry involved is quite messy, producing lots of sugars with no apparent biological use and only the tiniest bit of ribose. As such experimental results mounted, the plausibility of the formose reaction as the prebiotic sugar builder came into question. But the problem was that no one had established a reasonable alternative.




“We were thrown a lot of curve balls we had to really think through,” said Krisnamurthy of the years he spent working with postdoctoral fellow Vasu Sagi, who is lead author of the new paper. The team’s experiments revealed that under the right conditions, DHF and glyoxylate, when in the presence of a few other plausible prebiotic chemicals including formaldehyde, would produce sugars known as ketoses. Ketoses in turn can be converted to critical sugars, including some essential to forming certain amino acids, the DNA and RNA building blocks such as ribose.


In remarkable contrast to the formose reaction, which might only convert a fraction of a percent of its starting materials into ribose, the experiments Sagi slaved over, sometimes monitoring them 24 hours a day, gave clean conversion of DHF to ketoses.


Such efficiency is so rare in prebiotic chemistry and was so unexpected in the glyoxylate dihydroxyfumarate experiments, that the scientists were leery at first of their results. “We had to prove it by repeating the experiments many times,” said Sagi, but the results held.


“Prebiotic reactions are usually pretty messy, so when we saw how clean this was we were really pleasantly surprised,” said Krishnamurthy.

Interestingly, during the course of the work, Sagi and Krishnamurthy discovered DHF can react with itself to produce a new compounds never before documented, which the group reported separately late last year.



Interesting… formations of sugars, but what about the other things… phosphates?And what of the bonding?

Phosphorus is not found free in nature, but it is widely distributed in many minerals, mainly phosphates. Phosphate rock, which is partially made of apatite (an impure tri-calcium phosphate mineral), is an important commercial source of this element. About 50 percent of the global phosphorus reserves are in the Arab nations.[21] Large deposits of apatite are located in China, Russia, Morocco, Florida, Idaho, Tennessee, Utah, and elsewhere. Albright and Wilson in the United Kingdom and their Niagara Falls plant, for instance, were using phosphate rock in the 1890s and 1900s from the Îles du Connétable, Tennessee and Florida; by 1950 they were using phosphate rock mainly from Tennessee and North Africa.[22] In the early 1990s Albright and Wilson’s purified wet phosphoric acid business was being adversely affected by phosphate rock sales by China and the entry of their long-standing Moroccan phosphate suppliers into the purified wet phosphoric acid business.[23]

In 2012, the USGS estimated 71 billion tons of world reserves, where reserve figures refer to the amount assumed recoverable at current market prices; 0.19 billion tons were mined in 2011.[24]

Recent reports suggest that production of phosphorus may have peaked, leading to the possibility of global shortages by 2040.[25] In 2007, at the rate of consumption, the supply of phosphorus was estimated to run out in 345 years.[26] However, some scientists now believe that a “Peak phosphorus” will occur in 30 years and that “At current rates, reserves will be depleted in the next 50 to 100 years.”[27] Phosphorus comprises about 0.1% by mass of the average rock, and consequently the Earth’s supply is vast, although dilute.[10]



Phosphoric acid can be prepared by three routes – the thermal process, the wet process and the dry kiln process.

Thermal phosphoric acid

This very pure phosphoric acid is obtained by burning elemental phosphorus to produce phosphorus pentoxide and dissolving the product in dilute phosphoric acid. This produces a very pure phosphoric acid, since most impurities present in the rock have been removed when extracting phosphorus from the rock in a furnace. The end result is food-grade, thermal phosphoric acid; however, for critical applications, additional processing to remove arsenic compounds may be needed.

Earth being volcanic early on during the formation of life seems plausible.





“People have been discovering components of DNA in meteorites since the 1960’s,



Pasek and Lauretta began looking at meteorites as a possible source of the element. Meteorites contain several different phosphorus-bearing minerals, but the most important, said Pasek, is iron-nickel phosphide, also known as schreibersite. This metallic compound is extremely rare on Earth, but iron meteorites are peppered with schreibersite grains or even pinkish-colored veins of the mineral. Iron meteorites became the focus of the study because schreibersite is between 10 and 100 times more common in iron meteorites than other types.


Last April, Pasek, Lauretta, and undergraduate student Virginia Smith, mixed schriebersite with de-ionized water at room temperature. They then analyzed the liquid mixture using nuclear magnetic resonance. “We saw a whole slew of different phosphorus compounds being formed,” Pasek said. “One of the most interesting ones we found was P2O7, one of the more biochemically useful forms of phosphate, similar to what’s found in ATP.” The analysis revealed numerous phosphate salts in different states of oxidation, Pasek told Astronomy.


Previous experiments have formed P2O7, or pyrophosphate, but at high temperature or under other extreme conditions. “This allows us to somewhat constrain where the origins of life may have occurred,” Pasek said. “If you are going to have phosphate-based life, it likely would have had to occur near a freshwater region where a meteorite had recently fallen. We can go so far, maybe, as to say it was an iron meteorite.”


Meteorites were critical for the evolution of life, argues Pasek, because of minerals like pyrophosphate, which is used in ATP, in photosynthesis, in forming new phosphate bonds with carbon-bearing compounds, and in a variety of other biochemical processes.



One possibility, anyway… Also…


Exactly how and when organic molecules appeared in abundance on the young Earth, leading to the origin of life about 4 billion years ago, has been unclear. But new research suggests that meteor impacts could have created amino acids, the building blocks of life.



Creation.com’s reasons for why “RNA World” is implausible all use sources from the 1980s and going back…


Anywho…But let’s get back to the main question of “how did life begin” or rather how “did the organization of matter and energy resulting from a genetic sequence” begin?

‘It seems to me that RNA, under certain conditions, turned into DNA.


But the origin of RNA?


Now, Ernesto Di Mauro and colleagues found that ancient molecules called cyclic nucleotides can merge together in water and form polymers over 100 nucleotides long in water ranging from 40-90 °C — similar to water temperatures on ancient Earth.


Cyclic nucleotides like cyclic-AMP are very similar to the nucleotides that make up individual pieces of DNA or RNA (A, T, G and C), except that they form an extra chemical bond and assume a ring-shaped structure. That extra bond makes cyclic nucleotides more reactive, though, and thus they were able to join together into long chains at a decent rate (about 200 hours to reach 100 nucleotides long).



I just need… time and expertise to iron out the details.But… the science is plausible. Rna… Dna… At the beginning, I said if we have the origin of bacteria, then we have liftoff…



Artificial bacteria HAS been created before… but under what circumstances could it have arisen on its own?


All prokaryotes thus belong to  either the Eubacteria or the Archaebacteria; what is the difference? Add the domain of the eukaryotic organisms (protists, fungi, plants, and animals) and you can classify all living organisms on Earth. Archaebacteria emerged at least 3.5 billion years ago and are amongst the oldest life forms.There are several theories about the exact phylogenetic relationship (what was derived from what) between archaea, eukaryotes, and eubacteria, as can be seen in two versions of the Tree-of-Life. New insights dictate that eubacteria and archaebacteria diverged from one another near the time of the origin of life, and that eukaryotes were derived from archaea that had eubacteria living inside them.

Let’s ignore the details. Important is that bacteria (Eu and Archae) have been on earth much longer than eukaryotes; they are probably the oldest forms of life and have populated Earth for most of the time our planet exists. Going back in evolutionary history, the Archaea evolved some 3500 million years ago. Fossiles are mostly not quite as old as that, but occasionally we do find bacterial fossiles. Compare that to the age of the first eukaryotes, 1800 million years ago, or the first animals, 600 million years. Earth is truly the planet of bacteria in this respect!



Not sure how DNA first got their pill-shaped containers (cell walls)… but the experiment with the RNA from before sets a precedent for bacterial behavior, I believe. Wait… 

The cell wall is the tough, usually flexible but sometimes fairly rigid layer that surrounds some types of cells. It is located outside the cell membrane and provides these cells with structural support and protection, in addition to acting as a filtering mechanism. A major function of the cell wall is to act as a pressure vessel, preventing over-expansion when water enters the cell. Cell walls are found in plants, bacteria, fungi, algae, and some archaea. Animals and protozoa do not have cell walls.


The material in the cell wall varies between species, and can also differ depending on cell type and developmental stage. In bacteria, peptidoglycan forms the cell wall. Archaean cell walls have various compositions, and may be formed of glycoprotein S-layers, pseudopeptidoglycan, or polysaccharides. Fungi possess cell walls made of the glucosamine polymer chitin, and algae typically possess walls made of glycoproteins and polysaccharides. Unusually, diatoms have a cell wall composed of biogenic silica. Often, other accessory molecules are found anchored to the cell wall.



Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of bacteria (but not Archaea), forming the cell wall.



Sugar and amino acids, huh? Oh right… meteors. And the formation thereof?

The inner membrane of a bacterium is based on a lipid bilayer, and is semi-permeable, so that the principle metabolism of the cell is contained within that membrane. An important function of the bacterial cell wall is to resist the osmotic pressure gradients that would otherwise cause the continuous inner membrane to swell up and burst in water. Besides their inner membrane, gram negative bacteria also have a second, outer membrane which is not continuous but perforated with fairly large holes and, in some areas, adheres to the cell wall itself. These holes mean that large macromolecules can migrate across the outer membrane, so that most material from the external medium can exchange with that in the periplasmic space. At times, an outer “capsule” may also be present, surrounding the outer membrane. The material of the outer capsule is typically similar to that of the cell wall but it is much less concentrated or cross-linked and is not a rigid wall, rather it forms a gel beyond the outer membrane. Polymerized carbohydrate can also be found in the storage granules of some species. (Other species often have storage oil droplets.) Those storage granules are often surrounded by lipids but the nature of those lipids seems unclear and they do not seem to be arranged as a conventional bilayer.


The cell wall and the carbohydrate boundary layer are plainly very different from one another and one really has to look quite hard to find points of resemblance, but they do exist. Nonetheless, comparable chemistries do exist, or can be postulated, in both structures. So, the carbohydrate boundary layer can be compared with storage granules, with the bacterial cell wall and with the outer capsule. If one believes the idea of protocells as important intermediates in the evolutionary origin of life, then each of these structures is likely to arise either from the carbohydrate boundary layer or via analogous mechanisms.


The oil droplet has an outer surface who’s properties will quite resemble those of the outer surface of the inner membrane of the bacterium. Beyond the droplet surface there is a carbohydrate rich region and, we have argued, early glycolytic metabolism was concentrated between these regions as a sort of external metabolism. The corresponding region of the bacterium would be that between the inner membrane and the cell wall, the inner part of the periplasmic space.


Biochemists tend to think of metabolism as something that occurs within the inner membrane and the main metabolism does undoubtedly occur there. Nonetheless, it is equally clear that structures such as the cell wall, the outer membrane and the capsid could not exist unless some ongoing metabolism was building them and that metabolism must be occurring externally to the cytoplasm and the inner membrane. Hence, forms of metabolism do occur in the inner periplasmic space, between the membrane and the wall of bacteria, and also between the two membranes of gram negative bacteria. So, to some extent, bacteria do exhibit an external metabolism and metabolic pathways can operate outside the cell’s plasma membrane. Thus, the external metabolism of carbohydrate-bounded oil droplets does have some precedent.

http://www.evolution-origin.co.uk/p/a.php?q=peb106_protocells_cellsThen outside the cell wall is the Capsule outside the cell wall….

The cell capsule is a very large structure of some prokaryotic cells, such as bacterial cells. …It usually consists of polysaccharides,[1] but can be composed of other materials (e.g., polypeptide in B. anthracis).



Polysaccharides are long carbohydrate molecules of repeated monomer units joined together by glycosidic bonds. They range in structure from linear to highly branched.



We found organic carbon on Mars, so we KNOW they can occur naturally. Actually…


Although organic compounds are commonly found in meteorites and cometary samples, their origins presented a mystery. Now Ciesla and Sandford describe how the compounds possibly evolved in the March 29 edition of Science Express. How important a role these compounds may have played in giving rise to the origin of life remains poorly understood, however.


Sandford has devoted many years of laboratory research to the chemical processes that occur when high-energy ultraviolet radiation bombards simple ices like those seen in space. “We’ve found that a surprisingly rich mixture of organics is made,” Sandford said.

These include molecules of biological interest, such as amino acids, nucleobases and amphiphiles, which make up the building blocks of proteins, RNA and DNA, and cellular membranes, respectively. Irradiated ices should have produced these same sorts of molecules during the formation of the solar system, he said.


But a question remained: Could icy grains traveling through the outer edges of the solar nebula, in temperatures as low as minus-405 degrees Fahrenheit (less than 30 Kelvin), become exposed to UV radiation from surrounding stars?


Ciesla’s computer simulations reproduced the turbulent environment expected in the protoplanetary disk. This washing machine action mixed the particles throughout the nebula, and sometimes lofted them to high altitudes within the cloud, where they could become irradiated.

“Taking what we think we know about the dynamics of the outer solar nebula, it’s really hard for these ice particles not to spend at least part of their time where they’re going to be exposed to UV radiation,” Ciesla said.


The grains also moved in and out of warmer regions in the nebula. This completes the recipe for making organic compounds: ice, irradiation and warming.

“It was surprising how all these things just naturally fell out of the model,” Ciesla said. “It really did seem like this was a natural consequence of particle dynamics in the initial stage of planet formation.”



So we have organics… and all the material for the DNA/RNA of what could have developed into simple bacteria, but what of the INSIDES of a cell?


The cytoplasm inside the caspule is about 70% to 90% water and usually transparent.

Cytoplasm is made up of mostly water however the cytoplasm does contain proteins, vitamins, ions, nucleic acids, amino acids sugars, carbohydrates, and fatty acids. Oh, okay… makes sense. Anyway…


Single cells, one or more that could replicate…. replicate… replicate… mutate…. then some became multicellular.

Cells evolving multi-cellularity has been observed.


“A cluster alone isn’t multi-cellular,” Ratcliff says. “But when cells in a cluster cooperate, make sacrifices for the common good, and adapt to change, that’s an evolutionary transition to multi-cellularity.”



More than 500 million years ago, single-celled organisms on Earth’s surface began forming multi-cellular clusters that ultimately became plants and animals.  Just how that happened is a question that has eluded evolutionary biologists. Now, scientists have replicated that key step in the laboratory using common Brewer’s yeast, a single-celled organism.


The yeast “evolved” into multi-cellular clusters that work together cooperatively, reproduce and adapt to their environment–in essence, they became precursors to life on Earth as it is today.The results are published in this week’s issue of the journal Proceedings of the National Academy of Sciences (PNAS).



Okay… from  there grew 4 distinct “patterns of multi-cellularity” which became… fungi, plants, and animals… (and sometimes Archaea.)

Then from THOSE patterns, more patterns of division, more division, more division, more division…Then, some life grew into land off of rocks on the surface, then produced oxygen. And then OTHER cells formed a symbiotic relationship with those cells. The ones that could survive in an oxygen-rich environment. Oxygen wasn’t always on Earth…


Pyrite oxidation is a simple chemical process driven by two things: bacteria and oxygen. The researchers say this proves that oxygen levels in Earth’s atmosphere increased dramatically during that time.


“Aerobic bacteria broke down the pyrite, which released acid that dissolved rocks and soils into a cocktail of metals, including chromium,” says Konhauser. “The minerals were then carried to the oceans by the run-off of rain water.

“Our examination of the ancient seabed data shows the chromium levels increased significantly 2.48 billion years ago,” said Konhauser. “This gives us a new date for the Great Oxidation Event, the time when the atmosphere first had oxygen.”



There is evidence that some microbial life had migrated from Earth’s oceans to land by 2.75 billion years ago, though many scientists believe such land-based life was limited because the ozone layer that shields against ultraviolet radiation did not form until hundreds of millions years later.


But new research from the University of Washington suggests that early microbes might have been widespread on land, producing oxygen and weathering pyrite, an iron sulfide mineral, which released sulfur and molybdenum into the oceans.


“This shows that life didn’t just exist in a few little places on land. It was important on a global scale because it was enhancing the flow of sulfate from land into the ocean,” said Eva Stüeken, a UW doctoral student in Earth and space sciences.



Looks like we have an example of life changing the composition of the atmosphere… But… how does Ozone form?

Ozone is formed from dioxygen by the action of ultraviolet light and also atmospheric electrical discharges, and is present in low concentrations throughout the Earth’s atmosphere. In total, ozone makes up only 0.6 parts per million of the atmosphere.



Easy enough…More division, more division, more division…Mutation…

Mutations in DNA sequences generally occur through one of two processes:

  1. DNA damage from environmental agents such as ultraviolet light (sunshine), nuclear radiation or certain chemicals
  2. Mistakes that occur when a cell copies its DNA in preparation for cell division.




Chromosome #2 (http://www.youtube.com/watch?v=l0TunodLjRs)  … then… Ring speciation…  (http://www.youtube.com/watch?v=Pb6Z6NVmLt8)  some extinction… More division… then…NOW.

…Look around us.

All the diversity of life we see. Stop and think… all life you can see with your naked eyes are colonies of single celled organisms.

Sperm cell + egg cell x time = you.








  • Our planet had the tools to produce RNA.
  • RNA formed. Could reproduce. ( http://www.ted.com/talks/martin_hanczyc_the_line_between_life_and_not_life.html )
  • Under certain conditions, some RNA turned to DNA
  • Some DNA combinations became conducive to forming chemical layers of around it which would make it bacterial.
  • Mutations galore in pre-ozone Earth. And reduced to reasonable levels post-ozone.
  • Bacteria replicated. Mutated. 
  • Different DNA combinations produced different chemical behaviors. Including multi-cellularity.
  • Different “patterns” emerged in multi-cellular structures. These became the different kingdoms of life. Including Animals.
  • ( http://www.sciencedaily.com/releases/2011/12/111222142444.htm ) Chinese Fossils Shed Light On Evolutionary Origin of Animals from Single-Cell Ancestors
  • ( http://www.sciencedaily.com/releases/2008/04/080410153648.htm) The First Animal On Earth Was Significantly More Complex Than Previously Believed 
  • (Note: Evolution can sometimes make things more simple instead of more complex)
  • New DNA strands made bacteria conducive to making it to surface. Broke down certain chemicals/rocks. Produced oxygen. Oxygen + UV = Ozone
  • More land based bacteria, multiple-celled structures, more oxygen, more ozone…  then certain animals and some plants made it to surface in oxygen-rich environment.
  • To this day, all living things need to be connected to water to survive.
  • Mutations, Division, Speciation, Death, Decomposition, Consumption, Extinction …
  • Etc.
  • Present Day.

And the potential reality of EACH of these steps has been demonstrated here in this written piece.


This makes me realize….

  • I’m filled with sense of wonder to think we were all helping each other make it from the very beginning, especially with the oxygen thing. It really struck me.
  • We can see there was no singular point where “BAM!” life began.
  • It’s all a gradual process. We’re all a work in progress. 
  • Definitions are important.
  • The line between life and non-life is foggier than thought, when we think of the chemicals we’re made of. (An organization of matter and energy resulting from a genetic sequence.)
  • DNA…RNA… GNA… TNA… (last one was a joke)  But genes can be made of many things. Makes me wonder about String Theory. If we can include them in our definition of a “genetic sequence,” can our universe be classified as “living”?
  • Makes me realize how it important it is to consider what we put on and inside of our bodies.
  • Oils, sugar, water, sunlight, carbs…
  • The transformation of single celled to multi-celled is observable every time conception and subsequent birth place.
  • Re-contextualizes my preference for adopting and not wanting to pass on any of my genetic problems.
  • Re-contextualizes the METAL GEAR SOLID series. 
  • Re-contextualizes the realization that there’s more to life than passing on genes…. because we’ve evolved to recognize and realize things that are more important than short term spreading of genes. 
  • http://www.sciencedaily.com/releases/2008/07/080717201837.htm (Natural Selection May Not Produce The Best Organisms)
  • http://www.sciencedaily.com/releases/2011/03/110327191044.htm (Evolution: Not Only the Fittest Survive)
  • Re-contextualizes “Escaping from the Cave”  Because we did more than that… we evolved EYES.
  • There was more than a primordial soup that created us… but a COSMIC soup.
  • What are the odds, though? Idk, but apparently there are likely billions of Earth-like planets in our Milky Way Galaxy alone…
  • Re-contextualizes “We are a way for the cosmos to know itself” 
  • I realize that evolution is JUST as much about cooperation as it is about competition, if not moreso.
  • Considering the possibility that “we are a way for the cosmos to LOVE itself.”


I hunger. Time to consume plant/animal matter that the cells in my body can work together to break down into usable components, then absorb.


…that I may LIVE.