“Primordial Bounds”

“Primordial Bounds”

Animating forces danced in the abyss
From cosmic clouds did Helios arise
Upon the sands of Gaia shining bright
Warming seas to hold her in embrace
Effervescent stirrings in the depths below
From whence primordial bounds emerged
Tendril seeds could then begin to grow
Entropic channels out of chaos born
Spreading far and wide, were favored so
The spark of life ignited, on it goes
Destined imperfections bringing forth
Beauty and a mass of creatures flow

Senses born, interpretations formed
Rosetta stone with energetic tone
Neuronal trees to carve the world of one
Integrated symphony, the source of all divinity
Then the eye began to gaze within
Branches twisted, turned, and formed the self
Archetypal images and dreams to undergo
Ego and unconsciousness, a battle for the soul
Psyches feeding culture with the food of all the gods
Imagination, future selves, to suffer and rejoice
Cogitation flowing, individuation growing
‘Til cybernetic unity subsumes the human story

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“Celestial Dream”

Eyes laid on the stars above, a cosmic web, celestial dream
Chalice of life and death I see, chaos and form, dualities be
I see the One, self-aware, consciousness within a stream
Entropy, masquerading there, to blackness from the beam
Fabric of space, broadening sea, declaring to all it’s feeling free

Imagination manifest, with cooling down, primordial stew
Was, is, the yet to be, amalgamate the temporal me
Transformation, condensation, forces know just what to do
Clouds of gas, the stars are born, matter’s bound with much ado
Animate Being, an intricate tree, diverse au naturel decree

Psyches springing up anew, it simulates, the thoughts of “I”
The sense of self, but how could it be? Because of the power, because of the qi
Magical ocean, twinkling tide, reflecting from below the sky
Creatures abound, predator prey, appreciate before we die
Limited life, though infinite being, an optimistic view is key

The Origin and Evolution of Life: Part II

Even though life appears to be favorable in terms of the second law of thermodynamics (as explained in part one of this post), there have still been very important questions left unanswered regarding the origin of life including what mechanisms or platforms it could have used to get itself going initially.  This can be summarized by a “which came first, the chicken or the egg” dilemma, where biologists have wondered whether metabolism came first or if instead it was self-replicating molecules like RNA that came first.

On the one hand, some have argued that since metabolism is dependent on proteins and enzymes and the cell membrane itself, that it would require either RNA or DNA to code for those proteins needed for metabolism, thus implying that RNA or DNA would have to originate before metabolism could begin.  On the other hand, even the generation and replication of RNA or DNA requires a catalytic substrate of some kind and this is usually accomplished with proteins along with metabolic driving forces to accomplish those polymerization reactions, and this would seem to imply that metabolism along with some enzymes would be needed to drive the polymerization of RNA or DNA.  So biologists we’re left with quite a conundrum.  This was partially resolved when several decades ago, it was realized that RNA has the ability to not only act as a means of storing genetic information just like DNA, but it also has the additional ability of catalyzing chemical reactions just like an enzyme protein can.  Thus, it is feasible that RNA could act as both an information storage molecule as well as an enzyme.  While this helps to solve the problem if RNA began to self-replicate itself and evolve over time, the problem still remains of how the first molecules of RNA formed, because it seems that some kind of non-RNA metabolic catalyst would be needed to drive this initial polymerization.  Which brings us back to needing some kind of catalytic metabolism to drive these initial reactions.

These RNA polymerization reactions may have spontaneously formed on their own (or evolved from earlier self-replicating molecules that predated RNA), but the current models of how the early pre-biotic earth would have been around four billion years ago seem to suggest that there would have been too many destructive chemical reactions that would have suppressed the accumulation of any RNA and would have likely suppressed other self-replicating molecules as well.  What seems to be needed then is some kind of a catalyst that could create them quickly enough such that they would be able to accumulate in spite of any destructive reactions present, and/or some kind of physical barrier (like a cell wall) that protects the RNA or other self-replicating polymers so that they don’t interact with those destructive processes.

One possible solution to this puzzle that has been developing over the last several years involves alkaline hydrothermal vents.  We actually didn’t know that these kinds of vents existed until the year 2000 when they were discovered on a National Science Foundation expedition in the mid-Atlantic.  Then a few years later they were studied more closely to see what kinds of chemistries were involved with these kinds of vents.  Unlike the more well-known “black smoker” vents (which were discovered in the 1970’s), these alkaline hydrothermal vents have several properties that would have been hospitable to the emergence of life back during the Hadeon eon (between 4.6 and 4 billion years ago).

The ocean water during the Hadeon eon would have been much more acidic due to the higher concentrations of carbon dioxide (thus forming carbonic acid), and this acidic ocean water would have mixed with the hydrogen-rich alkaline water found within the vents, and this would have formed a natural proton gradient within the naturally formed pores of these rocks.  Also, electron transfer would have likely occurred when the hydrogen and methane-rich vent fluid contacted the carbon dioxide-rich ocean water, thus generating an electrical gradient.  This is already very intriguing because all living cells ultimately derive their metabolic driving forces from proton gradients or more generally from the flow of some kind of positive charge carrier and/or electrons.  Since the rock found in these vents undergoes a process called surpentization, which spreads the rock apart into various small channels and pockets, many different kinds of pores form in the rocks, and some of them would have been very thin-walled membranes separating the acidic ocean water from the alkaline hydrogen.  This would have facilitated the required semi-permeable barrier that modern cells have which we expect the earliest proto-cells to also have, and it would have provided the necessary source of energy to power various chemical reactions.

Additionally, these vents would have also provided a source of minerals (namely green rust and molybdenum) which likely would have behaved as enzymes, catalyzing reactions as various chemicals came into contact with them.  The green rust could have allowed the use of the proton gradient to generate molecules that contained phosphate, which could have stored the energy produced from the gradient — similar to how all living systems that we know of store their energy in ATP (Adenosine Tri-Phosphate).  The molybdenum on the other hand would have assisted in electron transfer through those membranes.

So this theory provides a very plausible way for catalytic metabolism as well as proto-cellular membrane formation to have resulted from natural geological processes.  These proto-cells would then likely have begun concentrating simple organic molecules formed from the reaction of CO2 and H2 with all the enzyme-like minerals that were present.  These molecules could then react with one another to polymerize and form larger and more complex molecules including eventually nucleotides and amino acids.  One promising clue that supports this theory is the fact that every living system on earth is known to share a common metabolic system, known as the citric acid cycle or Kreb’s cycle, where it operates in the forward direction for aerobic organisms and in the reverse direction for anaerobic organisms.  Since this cycle consists of only 11 molecules, and since all biological components and molecules that we know of in any species have been made by some number or combination of these 11 fundamental building blocks, scientists are trying to test (among other things) whether or not they can mimic these alkaline hydrothermal vent conditions along with the acidic ocean water that would have been present in the Hadrean era and see if it will precipitate some or all of these molecules.  If they can, it will show that this theory is more than plausible to account for the origin of life.

Once these basic organic molecules were generated, eventually proteins would have been able to form, some of which that could have made their way to the membrane surface of the pores and acted as pumps to direct the natural proton gradient to do useful work.  Once those proteins evolved further, it would have been possible and advantageous for the membranes to become less permeable so that the gradient could be highly focused on the pump channels on the membrane of these proto-cells.  The membrane could have begun to change into one made from lipids produced from the metabolic reactions, and we already know that lipids readily form micelles or small closed spherical structures once they aggregate in aqueous conditions.  As this occurred, the proto-cells would no longer have been trapped in the porous rock, but would have eventually been able to slowly migrate away from the vents altogether, eventually forming the phospholipid bi-layer cell membranes that we see in modern cells.  Once this got started, self-replicating molecules and the rest of the evolution of the cell would have underwent natural selection as per the Darwinian evolution that most of us are familiar with.

As per the earlier discussion regarding life serving as entropy engines and energy dissipation channels, this self-replication would have been favored thermodynamically as well because replicating those entropy engines and the energy dissipation channels means that they will only become more effective at doing so.  Thus, we can tie this all together, where natural geological processes would have allowed for the required metabolism to form, thus powering organic molecular synthesis and polymerization, and all of these processes serving to increase entropy and maximize energy dissipation.  All that was needed for this to initiate was a planet that had common minerals, water, and CO2, and the natural geological processes can do the rest of the work.  These kinds of planets actually seem to be fairly common in our galaxy, with estimates ranging in the billions, thus potentially harboring life (or where it is just a matter of time before it initiates and evolves if it hasn’t already).  While there is still a lot of work to be done to confirm the validity of these models and to try to find ways of testing them vigorously, we are getting relatively close to solving the puzzle of how life originated, why it is the way it is, and how we can better search for it in other parts of the universe.

The Origin and Evolution of Life: Part I

In the past, various people have argued that life originating at all let alone evolving higher complexity over time was thermodynamically unfavorable due to the decrease in entropy involved with both circumstances, and thus it was believed to violate the second law of thermodynamics.  For those unfamiliar with the second law, it basically asserts that the amount of entropy (often referred to as disorder) in a closed system tends to increase over time, or to put it another way, the amount of energy available to do useful work in a closed system tends to decrease over time.  So it has been argued that since the origin of life and the evolution of life with greater complexity would entail decreases in entropy, these events are therefore either at best unfavorable (and therefore the result of highly improbable chance), or worse yet they are altogether impossible.

We’ve known for quite some time now that these thermodynamic arguments aren’t at all valid because earth isn’t a thermodynamically closed or isolated system due to the constant supply of energy we receive from the sun.  Because we get a constant supply of energy from the sun, and because the entropy increase from the sun far outweighs the decrease in entropy produced from all biological systems on earth, the net entropy of the entire system increases and thus fits right in line with the second law as we would expect.

However, even though the emergence and evolution of life on earth do not violate the second law and are thus physically possible, that still doesn’t show that they are probable processes.  What we need to know is how favorable the reactions are that are required for initiating and then sustaining these processes.  Several very important advancements have been made in abiogenesis over the last ten to fifteen years, with the collaboration of geologists and biochemists, and it appears that they are in fact not only possible but actually probable processes for a few reasons.

One reason is that the chemical reactions that living systems undergo produce a net entropy as well, despite the drop of entropy associated with every cell and/or it’s arrangement with respect to other cells.  This is because all living systems give off heat with every favorable chemical reaction that is constantly driving the metabolism and perpetuation of those living systems. This gain in entropy caused by heat loss more than compensates for the loss in entropy that results with the production and maintenance of all the biological components, whether lipids, sugars, nucleic acids or amino acids and more complex proteins.  Beyond this, as more complexity arises during the evolution of the cells and living systems, the entropy that those systems produce tends to increase even more and so living systems with a higher level of complexity appear to produce a greater net entropy (on average) than less complex living systems.  Furthermore, once photosynthetic organisms evolved in particular, any entropy (heat) that they give off in the form of radiation ends up being of lower energy (infrared) than the photons given off by the sun to power those reactions in the first place.  Thus, we can see that living systems effectively dissipate the incoming energy from the sun, and energy dissipation is energetically favorable.

Living systems seem to serve as a controllable channel of energy flow for that energy dissipation, just like lightning, the eye of a hurricane, or a tornado, where high energy states in the form of charge gradients or pressure or temperature gradients end up falling to a lower energy state by dissipating that energy through specific focused channels that spontaneously form (e.g. individual concentrated lightning bolts, the eye of a hurricane, vortices, etc.).  These channels for energy flow are favorable and form because they allow the energy to be dissipated faster since the channels are initiated by some direction of energy flow that is able to self-amplify into a path of decreasing resistance for that energy dissipation.  Life and the metabolic processes involved with it, seem to direct energy flow in ways that are very similar to these other naturally arising processes in non-living physical systems.  Interestingly enough, a relevant hypothesis has been proposed for why consciousness and eventually self-awareness would have evolved (beyond the traditional reasons proposed by natural selection).  If an organism can evolve the ability to predict where energy is going to flow, where an energy dissipation channel will form (or form more effective ones themselves), conscious organisms can then behave in ways that much more effectively dissipate energy even faster (and also by catalyzing more entropy production), thus showing why certain forms of biological complexity such as consciousness, memory, etc., would have also been favored from a thermodynamic perspective.

Thus, the origin of life as well as the evolution of biological complexity appears to be increasingly favored by the second law, thus showing a possible fundamental physical driving force behind the origin and evolution of life.  Basically, the origin and evolution of life appear to be effectively entropy engines and catalytic energy dissipation channels, and these engines and channels produce entropy at a greater rate than the planet otherwise would in the absence of that life, thus showing at least one possible driving force behind life, namely, the second law of thermodynamics.  So ironically, not only does the origin and evolution of life not violate the second law of thermodynamics, but it actually seems to be an inevitable (or at least favorable) result because of the second law.  Some of these concepts are still being developed in various theories and require further testing to better validate them but they are in fact supported by well-established physics and by consistent and sound mathematical models.

Perhaps the most poetic concept I’ve recognized with these findings is that life is effectively speeding up the heat death of the universe.  That is, the second law of thermodynamics suggests that the universe will eventually lose all of its useful energy when all the stars burn out and all matter eventually spreads out and decays into lower and lower energy photons, and thus the universe is destined to undergo a heat death.  Life, because it is producing entropy faster than the universe otherwise would in the absence of that life, is actually speeding up this inevitable death of the universe, which is quite fascinating when you think about it.  At the very least, it should give a new perspective to those that ask the question “what is the meaning or purpose of life?”  Even if we don’t think it is proper to think of life as having any kind of objective purpose in the universe, what life is in fact doing is accelerating the death of not only itself, but of the universe as a whole.  Personally, this further reinforces the idea that we should all ascribe our own meaning and purpose to our lives, because we should be enjoying the finite amount of time that we have, not only as individuals, but as a part of the entire collective life that exists in our universe.

To read about the newest and most promising discoveries that may explain how life got started in the first place, read part two here.