The Highest Truth: Semiosis

If we exist as semiotic beings, then there must be semiotic principles inherent within the fabric of matter.

Mattering is a process which gives rise to what we call 'matter'. Sub-atomic particles like quarks (the smallest regular particle) protons, atoms, molecules, etc, appear in an almost infinite number in the universe; but wherever it appears, it is forced into being by the local context, which in turn is forced into being by a global (i.e. environmental) force around it.

Each object exists, but comes in and out of being at the lowest of levels.

As matter begins to consolidate, quite naturally, it exerts a greater force - a greater meaning - on the matter around it. Suns emerge, and the stuff they spew out in supernova explosions seeds a vast emptiness with massive amounts of matter.

The cooling off effect, or the distancing effect, allows more and more types of matter to come into being. This differentiation is, again, totally a function of the exertions of context. The quark is now stably present in the background - its nowhere near hot enough to create plasma; protons and neutrons emerge from quark-quark relations, and then together, as a nucleon, allows electrons to be pulled into their orbit, giving rise to yet another emergent property with greater mass: the atom.

Semiosis, a process, repeating itself inside the very fabric of things. Atoms can form two basic sorts of connections with one another: covalent (sharing hydrogen bonds) and ionic. All life occurs through covalent bonds, yet only some molecules are 'special' enough in their structure to support the emergence of life. Nucleic acids are special; kinetically tightly packed into crystalline-lattices, they are 'perfect' for stable replication of information in the form of constraints. But they are a later property of far more basic, thermodynamically driven 'redox chemistry' ,where the electron states of atoms shift, and so produce a net positive effect, 'work', for the system. Sulphur, Iron, and hydrogen, in all their different combinations, can yield electrons for life, and that is, according to Nick Lane, what probably happened. Somewhere in the deep sea over 4 billion years ago, in the micro-pores of alkaline olivine vents. The theory is, the ingredients existed for phosolipids to emerge; and when phospholipids emerge, the water-hating (hydrophobic) and water-loving parts, spread out far enough, closes in on itself, forming a vacuole.

Selection must have begun from here. The vacuole, the enclosure, is what 'decides' what is 'good', or coherent, and 'bad', or incoherent. The vacuole, of course, is made of molecules, and since molecules are typically unstable processes, the membrane falls apart unless it is able to channel into its insides the ingredients needed to reproduce the membrane. And this is indeed what happens. Early, one of the first and most consistent dynamics must have been this building up and falling apart of the vacuole, until the chemistry emerged - perhaps, due to some basic cross-interactions between the lithosphere (within the Earth) the hydrosphere (the oceans) and the atmosphere, exchanging their chemistries, producing a wide variety of molecules from which a stable vacuole could be reliably generated, and again and again.

Bit by bit, the geometry of space-time seems to 'know' when it hits upon a coherent organization. Symmetry - such as the ideal symmetry of a sphere - is a selection pressure upon the activities of the processes within the vacuole itself. To create life, three dimensions need to exist: at the core, the process driving it all is a core-metabolism made up of basic and widespread metabolites. These molecules must have been copious in number, deriving from chemistries coming up from the vents and the water around it. Overtime, as the system complexified, nucleic acids and amino acids found their place within the structure of the cell, generating what amounts to a 'communication system', a semiosis, whereby the dynamical coherency of the cell is stabilized by a 'building up' of a genetic library which records, registers, and chemically guides, the metabolic processes that are necessary for life. Oligomers (proteins, nucleic acids) are the 'memory' of 'what works' for living - that is, for channeling metabolic/chemical dynamics to produce a robust internal symmetry within the system.

So on the inside, in a nucleus (eventually) DNA responds to chemicals, which in turn receive their guidance from the way proteins studded in the membrane react to external chemistries. It's been argued (by lipton) that the membrane of the cell is the 'brain', insomuch as it is from this part of the cell which responds to the environment around it. Indeed, those proteins which don't become activated - because the nutrient needed to start the process isn't present - shrink in number, but the DNA process on the inside of the nucleus has a much longer longevity (which is why its in a nucleus!) This is akin to the difference between 'short term memory', or 'working memory', and long-term memory.

Finally, cofactors are molecules that are derived from the outside, and are essential to the activation of enzymatic proteins. These 3 parts: core metabolites, oligomers, and cofactors, make the life process: one part serves as the inner engine (core metabolism), the other part constructs a memory of 'what works' (nucleic acids, proteins), and the last part are chemical factors in the outside world which the system needs to stay in physical contact with if its going to survive.

Three is present at the planet level; three is present at the 'churning' level of the earth, ocean and atmosphere; three is present when the life process begins from three categories of chemical activity - one part being a general driver of chemical activity (via autocatalysis), another conserves those processes which work, and the last are those parts in the physical environment that supports growth and complexity. Three parts.

There is just one truth, and that truth is not you, or me, or what we think. We're far too behind - too ignorant - not to recognize that life precedes us and has a 'will' all of its own. The highest truth is the objective fact of what's evolving, and even more importantly, how it has evolved.

It has chosen three. The planet, the geospheres, the forms of chemical activity; forms of behavior. It keeps going, and will keep going, regardless of what we do.

Of course, that's not completely true. Here on earth, we could end it all. The third planet on the sun could be destroyed, simply because the elite human apes on this planet grew more and more out of line with the logic of nature. Or rather, with the nature of life. They fight it, they hate it, and they craft narratives to get as far away from the force of rationality - even though this method, this drive, is driven by a rational need generated by a rational, if unwitting, dissociation of the affective-social self from the positive presence and value of other human selves. This rationality - this fact - holds tightly, and no matter how much babbling has been produced by shoddy reasoning borne from dissociative processes that direct attention - the end is always the same. The end is the same for everyone.

End, Beginning. Tomato, Tamato. Potato, Patato.
Schlemiel, Schlimazel...Hasenpfeffer Incorporated!

a reply to: Astrocyte

Keep doing what you do. I enjoy your posts.

Patterns can be learned and applied to all facets of life.

yup....we have to in the end ofcourse.....rely on Him when that last breath goes out.....all that matters the clay cannot tell the potter what he will be

How Did Life Begin?

What do many scientists claim? Many who believe in evolution would tell you that billions of years ago, life began on the edge of an ancient tidal pool or deep in the ocean. They feel that in some such location, chemicals spontaneously assembled into bubblelike structures, formed complex molecules, and began replicating. They believe that all life on earth originated by accident from one or more of these “simple” original cells. [whereislogic: no evidence exists for these mythological "simple" original cells, often referred to as "protocells", they are as mythological as the flying spaghetti monster or pink unicorns, they are invoked as a requirement for the evolutionary storylines from simple to more complex, a clear direction unlike those claiming that evolution has no direction on other occasions when they aren't trying to sell the concept of "chemical evolution" a.k.a. "the chemical evolution theory of life", quoting Haldane&Oparin]

Other equally respected scientists who also support evolution disagree. They speculate that the first cells or at least their major components arrived on earth from outer space. Why? Because, despite their best efforts, scientists have been unable to prove that life can spring from nonliving molecules. In 2008, Professor of Biology Alexandre Meinesz highlighted the dilemma. He stated that over the last 50 years, “no empirical evidence supports the hypotheses of the spontaneous appearance of life on Earth from nothing but a molecular soup, and no significant advance in scientific knowledge leads in this direction.”1

What does the evidence reveal? The answer to the question, Where do babies come from? is well-documented and uncontroversial. Life always comes from preexisting life. However, if we go back far enough in time, is it really possible that this fundamental law was broken? Could life really spontaneously spring from nonliving chemicals? What are the chances that such an event could happen?

Researchers have learned that for a cell to survive, at least three different types of complex molecules must work together​—DNA (deoxyribonucleic acid), RNA (ribonucleic acid), and proteins. Today, few scientists would assert that a complete living cell suddenly formed by chance from a mix of inanimate chemicals. What, though, is the probability that RNA or proteins could form by chance? * [The probability of DNA forming by chance will be discussed in section 3, “Where Did the Instructions Come From?”]

Many scientists feel that life could arise by chance because of an experiment first conducted in 1953. In that year, Stanley L. Miller was able to produce some amino acids, the chemical building blocks of proteins, by discharging electricity into a mixture of gases that was thought to represent the atmosphere of primitive earth. Since then, amino acids have also been found in a meteorite. Do these findings mean that all the basic building blocks of life could easily be produced by chance?

“Some writers,” says Robert Shapiro, professor emeritus of chemistry at New York University, “have presumed that all life’s building blocks could be formed with ease in Miller-type experiments and were present in meteorites. This is not the case.”2 * [Professor Shapiro does not believe that life was created. He believes that life arose by chance in some fashion not yet fully understood. In 2009, scientists at the University of Manchester, England, reported making some nucleotides in their lab. However, Shapiro states that their recipe “definitely does not meet my criteria for a plausible pathway to the RNA world.”]

Psychology: The Art of selling nonsense-Miller Urey Experiment&Abiogenesis
Dr. Stephen Meyer: Chemistry/RNA World/crystal formation can't explain genetic information
Consider the RNA molecule. It is constructed of smaller molecules called nucleotides. A nucleotide is a different molecule from an amino acid and is only slightly more complex. Shapiro says that “no nucleotides of any kind have been reported as products of spark-discharge experiments or in studies of meteorites.”3 He further states that the probability of a self-replicating RNA molecule randomly assembling from a pool of chemical building blocks “is so vanishingly small that its happening even once anywhere in the visible universe would count as a piece of exceptional good luck.”4
[picture]
RNA (1) is required to make proteins (2), yet proteins are involved in the production of RNA. How could either one arise by chance, let alone both? Ribosomes (3) will be discussed in section 2.
[whereislogic: because I don't know how to link pictures: THE CENTRAL DOGMA -synra edition- English Narration

What about protein molecules? They can be made from as few as 50 or as many as several thousand amino acids bound together in a highly specific order. The average functional protein in a “simple” cell contains 200 amino acids. Even in those cells, there are thousands of different types of proteins. The probability that just one protein containing only 100 amino acids could ever randomly form on earth has been calculated to be about one chance in a million billion.

If the creation of complex molecules in the laboratory requires the skill of a scientist, could the far more complex molecules in a cell really arise by chance?

Researcher Hubert P. Yockey, who supports the teaching of evolution, goes further. He says: “It is impossible that the origin of life was ‘proteins first.’”5 RNA is required to make proteins, yet proteins are involved in the production of RNA. What if, despite the extremely small odds, both proteins and RNA molecules did appear by chance in the same place at the same time? How likely would it be for them to cooperate to form a self-replicating, self-sustaining type of life? “The probability of this happening by chance (given a random mixture of proteins and RNA) seems astronomically low,” says Dr. Carol Cleland *, a member of the National Aeronautics and Space Administration’s Astrobiology Institute. “Yet,” she continues, “most researchers seem to assume that if they can make sense of the independent production of proteins and RNA under natural primordial conditions, the coordination will somehow take care of itself.” Regarding the current theories of how these building blocks of life could have arisen by chance, she says: “None of them have provided us with a very satisfying story about how this happened.”6

*: Dr. Cleland is not a creationist. She believes that life arose by chance in some fashion not yet fully understood.

Why do these facts matter? Think of the challenge facing researchers who feel that life arose by chance. They have found some amino acids that also appear in living cells. In their laboratories, they have, by means of carefully designed and directed experiments, manufactured other more complex molecules. Ultimately, they hope to build all the parts needed to construct a “simple” cell. Their situation could be likened to that of a scientist who takes naturally occurring elements; transforms them into steel, plastic, silicone, and wire; and constructs a robot. He then programs the robot to be able to build copies of itself. By doing so, what will he prove? At best, that an intelligent entity can create an impressive machine.

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Sources 1-6

a reply to: whereislogic
Molecular Machinery of Life