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Conscious Realism & The Interface Theory of Perception

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A few months ago I was reading an interesting article in The Atlantic about Donald Hoffman’s Interface Theory of Perception.  As a person highly interested in consciousness studies, cognitive science, and the mind-body problem, I found the basic concepts of his theory quite fascinating.  What was most interesting to me was the counter-intuitive connection between evolution and perception that Hoffman has proposed.  Now it is certainly reasonable and intuitive to assume that evolutionary natural selection would favor perceptions that are closer to “the truth” or closer to the objective reality that exists independent of our minds, simply because of the idea that perceptions that are more accurate will be more likely to lead to survival than perceptions that are not accurate.  As an example, if I were to perceive lions as inert objects like trees, I would be more likely to be naturally selected against and eaten by a lion when compared to one who perceives lions as a mobile predator that could kill them.

While this is intuitive and reasonable to some degree, what Hoffman actually shows, using evolutionary game theory, is that with respect to organisms with comparable complexity, those with perceptions that are closer to reality are never going to be selected for nearly as much as those with perceptions that are tuned to fitness instead.  More so, truth in this case will be driven to extinction when it is up against perceptual models that are tuned to fitness.  That is to say, evolution will select for organisms that perceive the world in a way that is less accurate (in terms of the underlying reality) as long as the perception is tuned for survival benefits.  The bottom line is that given some specific level of complexity, it is more costly to process more information (costing more time and resources), and so if a “heuristic” method for perception can evolve instead, one that “hides” all the complex information underlying reality and instead provides us with a species-specific guide to adaptive behavior, that will always be the preferred choice.

To see this point more clearly, let’s consider an example.  Let’s imagine there’s an animal that regularly eats some kind of insect, such as a beetle, but it needs to eat a particular sized beetle or else it has a relatively high probability of eating the wrong kind of beetle (and we can assume that the “wrong” kind of beetle would be deadly to eat).  Now let’s imagine two possible types of evolved perception: it could have really accurate perceptions about the various sizes of beetles that it encounters so it can distinguish many different sizes from one another (and then choose the proper size range to eat), or it could evolve less accurate perceptions such that all beetles that are either too small or too large appear as indistinguishable from one another (maybe all the wrong-sized beetles whether too large or too small look like indistinguishable red-colored blobs) and perhaps all the beetles that are in the ideal size range for eating appear as green-colored blobs (that are again, indistinguishable from one another).  So the only discrimination in this latter case of perception is between red and green colored blobs.

Both types of perception would solve the problem of which beetles to eat or not eat, but the latter type (even if much less accurate) would bestow a fitness advantage over the former type, by allowing the animal to process much less information about the environment by not focusing on relatively useless information (like specific beetle size).  In this case, with beetle size as the only variable under consideration for survival, evolution would select for the organism that knows less total information about beetle size, as long as it knows what is most important about distinguishing the edible beetles from the poisonous beetles.  Now we can imagine that in some cases, the fitness function could align with the true structure of reality, but this is not what we ever expect to see generically in the world.  At best we may see some kind of overlap between the two but if there doesn’t have to be any then truth will go extinct.

Perception is Analogous to a Desktop Computer Interface

Hoffman analogizes this concept of a “perception interface” with the desktop interface of a personal computer.  When we see icons of folders on the desktop and drag one of those icons to the trash bin, we shouldn’t take that interface literally, because there isn’t literally a folder being moved to a literal trash bin but rather it is simply an interface that hides most if not all of what is really going on in the background — all those various diodes, resistors and transistors that are manipulated in order to modify stored information that is represented in binary code.

The desktop interface ultimately provides us with an easy and intuitive way of accomplishing these various information processing tasks because trying to do so in the most “truthful” way — by literally manually manipulating every diode, resistor, and transistor to accomplish the same task — would be far more cumbersome and less effective than using the interface.  Therefore the interface, by hiding this truth from us, allows us to “navigate” through that computational world with more fitness.  In this case, having more fitness simply means being able to accomplish information processing goals more easily, with less resources, etc.

Hoffman goes on to say that even though we shouldn’t take the desktop interface literally, obviously we should still take it seriously, because moving that folder to the trash bin can have direct implications on our lives, by potentially destroying months worth of valuable work on a manuscript that is contained in that folder.  Likewise we should take our perceptions seriously, even if we don’t take them literally.  We know that stepping in front of a moving train will likely end our conscious experience even if it is for causal reasons that we have no epistemic access to via our perception, given the species-specific “desktop interface” that evolution has endowed us with.

Relevance to the Mind-body Problem

The crucial point with this analogy is the fact that if our knowledge was confined to the desktop interface of the computer, we’d never be able to ascertain the underlying reality of the “computer”, because all that information that we don’t need to know about that underlying reality is hidden from us.  The same would apply to our perception, where it would be epistemically isolated from the underlying objective reality that exists.  I want to add to this point that even though it appears that we have found the underlying guts of our consciousness, i.e., the findings in neuroscience, it would be mistaken to think that this approach will conclusively answer the mind-body problem because the interface that we’ve used to discover our brains’ underlying neurobiology is still the “desktop” interface.

So while we may think we’ve found the underlying guts of “the computer”, this is far from certain, given the possibility of and support for this theory.  This may end up being the reason why many philosophers claim there is a “hard problem” of consciousness and one that can’t be solved.  It could be that we simply are stuck in the desktop interface and there’s no way to find out about the underlying reality that gives rise to that interface.  All we can do is maximize our knowledge of the interface itself and that would be our epistemic boundary.

Predictions of the Theory

Now if this was just a fancy idea put forward by Hoffman, that would be interesting in its own right, but the fact that it is supported by evolutionary game theory and genetic algorithm simulations shows that the theory is more than plausible.  Even better, the theory is actually a scientific theory (and not just a hypothesis), because it has made falsifiable predictions as well.  It predicts that “each species has its own interface (with some similarities between phylogenetically related species), almost surely no interface performs reconstructions (read the second link for more details on this), each interface is tailored to guide adaptive behavior in the relevant niche, much of the competition between and within species exploits strengths and limitations of interfaces, and such competition can lead to arms races between interfaces that critically influence their adaptive evolution.”  The theory predicts that interfaces are essential to understanding evolution and the competition between organisms, whereas the reconstruction theory makes such understanding impossible.  Thus, evidence of interfaces should be widespread throughout nature.

In his paper, he mentions the Jewel beetle as a case in point.  This beetle has a perceptual category, desirable females, which works well in its niche, and it uses it to choose larger females because they are the best mates.  According to the reconstructionist thesis, the male’s perception of desirable females should incorporate a statistical estimate of the true sizes of the most fertile females, but it doesn’t do this.  Instead, it has a category based on “bigger is better” and although this bestows a high fitness behavior for the male beetle in its evolutionary niche, if it comes into contact with a “stubbie” beer bottle, it falls into an infinite loop by being drawn to this supernormal stimuli since it is smooth, brown, and extremely large.  We can see that the “bigger is better” perceptual category relies on less information about the true nature of reality and instead chooses an “informational shortcut”.  The evidence of supernormal stimuli which have been found with many species further supports the theory and is evidence against the reconstructionist claim that perceptual categories estimate the statistical structure of the world.

More on Conscious Realism (Consciousness is all there is?)

This last link provided here shows the mathematical formalism of Hoffman’s conscious realist theory as proved by Chetan Prakash.  It contains a thorough explanation of the conscious realist theory (which goes above and beyond the interface theory of perception) and it also provides answers to common objections put forward by other scientists and philosophers on this theory.

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Darwin’s Big Idea May Be The Biggest Yet

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Back in 1859, Charles Darwin released his famous theory of evolution by natural selection whereby inherent variations in the individual members of some population of organisms under consideration would eventually lead to speciation events due to those variations producing a differential in survival and reproductive success and thus leading to the natural selection of some subset of organisms within that population.  As Darwin explained in his On The Origin of Species:

If during the long course of ages and under varying conditions of life, organic beings vary at all in the several parts of their organisation, and I think this cannot be disputed; if there be, owing to the high geometrical powers of increase of each species, at some age, season, or year, a severe struggle for life, and this certainly cannot be disputed; then, considering the infinite complexity of the relations of all organic beings to each other and to their conditions of existence, causing an infinite diversity in structure, constitution, and habits, to be advantageous to them, I think it would be a most extraordinary fact if no variation ever had occurred useful to each being’s own welfare, in the same way as so many variations have occurred useful to man. But if variations useful to any organic being do occur, assuredly individuals thus characterised will have the best chance of being preserved in the struggle for life; and from the strong principle of inheritance they will tend to produce offspring similarly characterised. This principle of preservation, I have called, for the sake of brevity, Natural Selection.

While Darwin’s big idea completely transformed biology in terms of it providing (for the first time in history) an incredibly robust explanation for the origin of the diversity of life on this planet, his idea has since inspired other theories pertaining to perhaps the three largest mysteries that humans have ever explored: the origin of life itself (not just the diversity of life after it had begun, which was the intended scope of Darwin’s theory), the origin of the universe (most notably, why the universe is the way it is and not some other way), and also the origin of consciousness.

Origin of Life

In order to solve the first mystery (the origin of life itself), geologists, biologists, and biochemists are searching for plausible models of abiogenesis, whereby the general scheme of these models would involve chemical reactions (pertaining to geology) that would have begun to incorporate certain kinds of energetically favorable organic chemistries such that organic, self-replicating molecules eventually resulted.  Now, where Darwin’s idea of natural selection comes into play with life’s origin is in regard to the origin and evolution of these self-replicating molecules.  First of all, in order for any molecule at all to build up in concentration requires a set of conditions such that the reaction leading to the production of the molecule in question is more favorable than the reverse reaction where the product transforms back into the initial starting materials.  If merely one chemical reaction (out of a countless number of reactions occurring on the early earth) led to a self-replicating product, this would increasingly favor the production of that product, and thus self-replicating molecules themselves would be naturally selected for.  Once one of them was produced, there would have been a cascade effect of exponential growth, at least up to the limit set by the availability of the starting materials and energy sources present.

Now if we assume that at least some subset of these self-replicating molecules (if not all of them) had an imperfect fidelity in the copying process (which is highly likely) and/or underwent even a slight change after replication by reacting with other neighboring molecules (also likely), this would provide them with a means of mutation.  Mutations would inevitably lead to some molecules becoming more effective self-replicators than others, and then evolution through natural selection would take off, eventually leading to modern RNA/DNA.  So not only does Darwin’s big idea account for the evolution of diversity of life on this planet, but the basic underlying principle of natural selection would also account for the origin of self-replicating molecules in the first place, and subsequently the origin of RNA and DNA.

Origin of the Universe

Another grand idea that is gaining heavy traction in cosmology is that of inflationary cosmology, where this theory posits that the early universe underwent a period of rapid expansion, and due to quantum mechanical fluctuations in the microscopically sized inflationary region, seed universes would have resulted with each one having slightly different properties, one of which that would have expanded to be the universe that we live in.  Inflationary cosmology is currently heavily supported because it has led to a number of predictions, many of which that have already been confirmed by observation (it explains many large-scale features of our universe such as its homogeneity, isotropy, flatness, and other features).  What I find most interesting with inflationary theory is that it predicts the existence of a multiverse, whereby we are but one of an extremely large number of other universes (predicted to be on the order of 10^500, if not an infinite number), with each one having slightly different constants and so forth.

Once again, Darwin’s big idea, when applied to inflationary cosmology, would lead to the conclusion that our universe is the way it is because it was naturally selected to be that way.  The fact that its constants are within a very narrow range such that matter can even form, would make perfect sense, because even if an infinite number of universes exist with different constants, we would only expect to find ourselves in one that has the constants within the necessary range in order for matter, let alone life to exist.  So any universe that harbors matter, let alone life, would be naturally selected for against all the other universes that didn’t have the right properties to do so, including for example, universes that had too high or too low of a cosmological constant (such as those that would have instantly collapsed into a Big Crunch or expanded into a heat death far too quickly for any matter or life to have formed), or even universes that didn’t have the proper strong nuclear force to hold atomic nuclei together, or any other number of combinations that wouldn’t work.  So any universe that contains intelligent life capable of even asking the question of their origins, must necessarily have its properties within the required range (often referred to as the anthropic principle).

After our universe formed, the same principle would also apply to each galaxy and each solar system within those galaxies, whereby because variations exist in each galaxy and within each substituent solar system (differential properties analogous to different genes in a gene pool), then only those that have an acceptable range of conditions are capable of harboring life.  With over 10^22 stars in the observable universe (an unfathomably large number), and billions of years to evolve different conditions within each solar system surrounding those many stars, it isn’t surprising that eventually the temperature and other conditions would be acceptable for liquid water and organic chemistries to occur in many of those solar systems.  Even if there was only one life permitting planet per galaxy (on average), that would add up to over 100 billion life permitting planets in the observable universe alone (with many orders of magnitude more life permitting planets in the non-observable universe).  So given enough time, and given some mechanism of variation (in this case, differences in star composition and dynamics), natural selection in a sense can also account for the evolution of some solar systems that do in fact have life permitting conditions in a universe such as our own.

Origin of Consciousness

The last significant mystery I’d like to discuss involves the origin of consciousness.  While there are many current theories pertaining to different aspects of consciousness, and while there has been much research performed in the neurosciences, cognitive sciences, psychology, etc., pertaining to how the brain works and how it correlates to various aspects of the mind and consciousness, the brain sciences (though neuroscience in particular) are in their relative infancy and so there are still many questions that haven’t been answered yet.  One promising theory that has already been shown to account for many aspects of consciousness is Gerald Edelman’s theory of neuronal group selection (NGS) otherwise known as neural Darwinism (ND), which is a large scale theory of brain function.  As one might expect from the name, the mechanism of natural selection is integral to this theory.  In ND, the basic idea consists of three parts as read on the Wiki:

  1. Anatomical connectivity in the brain occurs via selective mechanochemical events that take place epigenetically during development.  This creates a diverse primary neurological repertoire by differential reproduction.
  2. Once structural diversity is established anatomically, a second selective process occurs during postnatal behavioral experience through epigenetic modifications in the strength of synaptic connections between neuronal groups.  This creates a diverse secondary repertoire by differential amplification.
  3. Re-entrant signaling between neuronal groups allows for spatiotemporal continuity in response to real-world interactions.  Edelman argues that thalamocortical and corticocortical re-entrant signaling are critical to generating and maintaining conscious states in mammals.

In a nutshell, the basic differentiated structure of the brain that forms in early development is accomplished through cellular proliferation, migration, distribution, and branching processes that involve selection processes operating on random differences in the adhesion molecules that these processes use to bind one neuronal cell to another.  These crude selection processes result in a rough initial configuration that is for the most part fixed.  However, because there are a diverse number of sets of different hierarchical arrangements of neurons in various neuronal groups, there are bound to be functionally equivalent groups of neurons that are not equivalent in structure, but are all capable of responding to the same types of sensory input.  Because some of these groups should in theory be better than others at responding to some particular type of sensory stimuli, this creates a form of neuronal/synaptic competition in the brain, whereby those groups of neurons that happen to have the best synaptic efficiency for the stimuli in question are naturally selected over the others.  This in turn leads to an increased probability that the same network will respond to similar or identical signals in the future.  Each time this occurs, synaptic strengths increase in the most efficient networks for each particular type of stimuli, and this would account for a relatively quick level of neural plasticity in the brain.

The last aspect of the theory involves what Edelman called re-entrant signaling whereby a sampling of the stimuli from functionally different groups of neurons occurring at the same time leads to a form of self-organizing intelligence.  This would provide a means for explaining how we experience spatiotemporal consistency in our experience of sensory stimuli.  Basically, we would have functionally different parts of the brain, such as various maps in the visual centers that pertain to color versus others that pertain to orientation or shape, that would effectively amalgamate the two (previously segregated) regions such that they can function in parallel and thus correlate with one another producing an amalgamation of the two types of neural maps.  Once this re-entrant signaling is accomplished between higher order or higher complexity maps in the brain, such as those pertaining to value-dependent memory storage centers, language centers, and perhaps back to various sensory cortical regions, this would create an even richer level of synchronization, possibly leading to consciousness (according to the theory).  In all of the aspects of the theory, the natural selection of differentiated neuronal structures, synaptic connections and strengths and eventually that of larger re-entrant connections would be responsible for creating the parallel and correlated processes in the brain believed to be required for consciousness.  There’s been an increasing amount of support for this theory, and more evidence continues to accumulate in support of it.  In any case, it is a brilliant idea and one with a lot of promise in potentially explaining one of the most fundamental aspects of our existence.

Darwin’s Big Idea May Be the Biggest Yet

In my opinion, Darwin’s theory of evolution through natural selection was perhaps the most profound theory ever discovered.  I’d even say that it beats Einstein’s theory of Relativity because of its massive explanatory scope and carryover to other disciplines, such as cosmology, neuroscience, and even the immune system (see Edelman’s Nobel work on the immune system, where he showed how the immune system works through natural selection as well, as opposed to some type of re-programming/learning).  Based on the basic idea of natural selection, we have been able to provide a number of robust explanations pertaining to many aspects of why the universe is likely to be the way it is, how life likely began, how it evolved afterward, and it may possibly be the answer to how life eventually evolved brains capable of being conscious.  It is truly one of the most fascinating principles I’ve ever learned about and I’m honestly awe struck by its beauty, simplicity, and explanatory power.

DNA & Information: A Response to an Old ID Myth

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A common myth that goes around in Intelligent Design (creationist) circles is the idea that DNA can only degrade over time, and thus any and all mutations are claimed to be harmful and only serve to reduce “information” stored in that DNA.  The claim is specifically meant to suggest that evolution from a common ancestor is impossible by naturalistic processes because DNA wouldn’t have been able to form in the first place and/or it wouldn’t be able to grow or change to allow for speciation.  Thus, the claim implies that either an intelligent designer had to intervene and guide evolution every step of the way (by creating DNA, fixing mutations as they occurred or preventing them from happening, and then ceasing this intervention as soon as scientists began studying genetics), or it implies that all organisms must have been created all at once by an intelligent designer with DNA that was “intelligently” designed to fail and degrade over time (thus questioning the intelligence of this designer).

These claims have been refuted a number of times over the years by the scientific community with a consensus that’s been drawn from years of research in evolutionary biology among other disciplines, and the claims seem to be mostly a result of fundamental misunderstandings of biology (or intentional misrepresentations of the facts) and also the result of an improper application of information theory to biological processes.  What’s unfortunate is that these claims are still circulating around, largely because the propagators aren’t interested in reason, evidence, or anything that may threaten their beliefs in the supernatural, and so they simply repeat this non-sense to others without fact checking them and without any consideration as to whether the claims even appear to be rational or logically sound at all.

After having recently engaged in a discussion with a Christian that made this very claim (among many other unsubstantiated, faith-based assertions), I figured it would be useful to demonstrate why this claim is so easily refutable based on some simple thought experiments as well as some explanations and evidence found in the actual biological sciences.  First, let’s consider a strand of DNA with the following 12 nucleotide sequence (split into triplets for convenience):

ACT-GAC-TGA-CAG

If a random mutation occurs in this strand during replication, say, at the end of the strand, thus turning Guanine (G) to Adenine (A), then we’d have:

ACT-GAC-TGA-CAA

If another random mutation occurs in this string during replication, say, at the end of the string once again, thus turning Adenine (A) back to Guanine (G), then we’d have the original nucleotide sequence once again.  This shows how two random mutations could lead to the same original strand of genetic information, thus showing how it can lose its original information and have it re-created once again.  It’s also relevant to note that because there are 64 possible codons produced from the four available nucleotides (4^3 = 64), and since only 20 amino acids are needed to make proteins, there are actually several codons that code for any individual amino acid.

In the case given above, the complementary RNA sequence produced for the two sequences (before and after mutation) would be:

UGA-CUG-ACU-GUC (before mutation)
UGA-CUG-ACU-GUU (after mutation)

It turns out that GUC and GUU (the last triplets in these sequences) are both codons that code for the same amino acid (Valine), thus showing how a silent mutation can occur as well, where a silent mutation is one in which there are no changes to the amino acids or subsequent proteins that the sequence codes for (and thus no functional change in the organism at all).  The fact that silent mutations even exist also shows how mutations don’t necessarily result in a loss or change of information at all.  So in this case, as a result of the two mutations, the end result was no change in the information at all.  Had the two strands been different such that they actually coded for different proteins after the initial mutation, then the second mutation would have reversed this problem anyway thus re-creating the original information that was lost.  So this demonstration in itself already refutes the claim that DNA can only lose information over time, or that mutations necessarily lead to a loss of information.  All one needs are random mutations, and there will always be a chance that some information is lost and then re-created.  Furthermore, if we had started with a strand that didn’t code for any amino acid at all in the last triplet, and then the random mutation changed it such that it did code for an amino acid (such as Valine), this would be an increase in information regardless (since a new amino acid was expressed that was previously absent), although this depends on how we define information (more on that in a minute).

Now we could ask, is the mutation valuable, that is, conducive to the survival of the organism?  That would entirely depend on the internal/external environment of that organism.  If we changed the diet of the organism or the other conditions in which it lived, we could arrive at opposite conclusions.  Which goes to show that of the mutations that aren’t neutral (most mutations are neutral), those that are harmful or beneficial are often so because of the specific internal/external environment under consideration. If an organism is able to digest lactose exclusively and it undergoes a mutation that provides some novel ability of digesting sucrose at the expense of digesting lactose a little less effectively than before, this would be a harmful mutation if the organism lived in an environment with lactose as the only available sugar.  If however, the organism was already in an environment that had more sucrose than lactose available, then the mutation would obviously be beneficial for now the organism could exploit the most available food source.  This would likely lead to that mutation being naturally selected for and increasing its frequency in the gene pool of that organism’s local population.

Another thing that is often glossed over with the Intelligent Design (ID) claims about genetic information being lost is the fact that they first have to define what exactly information is necessarily before presenting the rest of their argument.  Whether or not information is gained or lost requires knowing how to measure information in the first place.  This is where other problems begin to surface with ID claims like these because they tend to leave this definition either poorly defined, ambiguous or conveniently malleable to serve the interests of their argument.  What we need is a clear and consistent definition of information, and then we need to check that the particular definition given is actually applicable to biological systems, and then we can check to see if the claim is true.  I have yet to see this actually demonstrated successfully.  I was able to avoid this problem in my example above, because no matter how information is defined, it was shown that two mutations can lead to the original nucleotide sequence (whatever amount of genetic “information” that may have been).  If the information had been lost, it was recreated, and if it wasn’t technically lost at all during the mutation, then it shows that not all mutations lead to a loss of information.

I would argue that a fairly useful and consistent way to define information in terms of its application to describing the evolving genetics of biological organisms would be to describe it as any positive correlation between the functionality that the genetic sequences code for and the attributes of the environment that the organism is contained in.  This is useful because it represents the relationship between the genes and the environment and it seems to fit in line with the most well-established models in evolutionary biology, including the fundamental concept of natural selection leading to favored genotypes.

If an organism has a genetic sequence such that it can digest lactose (as per my previous example), and it is within an environment that has a supply of lactose available, then whatever genes are responsible for that functionality are effectively a form of information that describes or represents some real aspects of the organism’s environment (sources of energy, chemical composition, etc.).  The more genes that do this, that is, the more complex and specific the correlation, the more information there is in the organism’s genome.  So for example, if we consider the aforementioned mutation that caused the organism to develop a novel ability to digest sucrose in addition to lactose, then if it is in an environment that has both lactose and sucrose, this genome has even more environmental information stored within it because of the increased correlation between that genome and the environment.  If the organism can most efficiently digest a certain proportion of lactose versus sucrose, then if this optimized proportion evolves to approach the actual proportion of sugars in the environment around that organism (e.g. 30% lactose, 70% sucrose), then once again we have an increase in the amount of environmental information contained within its genome due to the increase in specificity.

Defining information in this way allows us to measure degrees of how well-adapted a particular organism is (even if only one trait or attribute at a time) to its current environment as well as its past environment (based on what the convergent evidence suggests) and it also provides at least one way to measure how genetically complex the organism is.

So not only are the ID claims about genetic information easily refuted with the inherent nature of random mutations and natural selection, but we can also see that the claims are further refuted once we define genetic information such that it encompasses the fundamental relationship between genes and the environment they evolve in.

The Origin and Evolution of Life: Part II

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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

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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.

A Scientific Perspective of the Arts

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Science and the arts have long been regarded as mutually exclusive domains, where many see artistic expression as something that science can’t explain or reduce in any way, or as something that just shouldn’t be explored by any kind of scientific inquiry.  To put it another way, many people have thought it impossible for there to ever be any kind of a “science of the arts”.  The way I see it, science isn’t something that can be excluded from any domain at all, because we apply science in a very general way every time we learn or conceive of new ideas, experiment with them, and observe the results to determine if we should modify our beliefs based on those experiences.  Whenever we pose a question about anything we experience, in the attempt to learn something new and gain a better understanding about those experiences, a scientific approach (based on reason and the senses) is the only demonstrably reliable way we’ve ever been able to arrive at any kind of meaningful answer.  The arts are no exception to this, and in fact, many questions that have been asked about the arts and aesthetics in general have not only been answered by an application of the aforementioned general scientific reasoning that we use every day, but have in fact also been answered within many specific well-established branches of science.

Technology & The Scientific Method

It seems to me that the sciences and the various rewards we’ve reaped from them have influenced art in a number of ways and even facilitated new variations of artistic expression.  For example, science has been applied to create the very technologies used in producing art.  The various technologies created through the application of science have been used to produce new sounds (and new combinations thereof), new colors (and new color gradients), new shapes, and various other novel visual effects.  We’ve even used them to produce new tastes and smells (in the culinary arts for example).  They’ve also been used to create entirely new media through which art is exemplified.  So in a large number of ways, any kind of art has been dependent on science in some way or another — even by simply applying the scientific method by hypothesizing a way to express art in some way, even through a new medium or with a new technique, where the artist experiments with that medium or technique to see if it is satisfactory, and then modifies their hypothesis if needed until the artist obtains the desired result for what they’re trying to express (whether through simple trial and error or what-have-you).

Evolutionary Factors Influencing Aesthetic Preferences

Then we have the questions that pertain to whether or not aesthetic preferences are solely subjective and individualistic, or if they are also objective in some ways.  Some of these questions have in fact been explored within the fields of evolutionary biology and psychology (and within the field of psychology in general), where it is well known that humans find certain types of perceptions pleasurable, such as environments and objects that are conducive to our survival.  For example, the majority of people enjoy visually perceiving an abundance of food, fresh water and plush vegetation, healthy social relationships (including sex) and various emotions, etc. There are also various sounds, smells, tastes, and even tactile sensations that we’ve evolved to find pleasurable — such as the sound of laughter, flowing water, or rain, the taste of salt, fat, and sugar, the smell of various foods and plants, or the tactile sensation of sexual stimulation (to give but a few examples).  So it’s not surprising that many forms of art can appeal to the majority of people by employing these kinds of objects and environments within them, especially in cases where these sources of pleasurable sensations are artificially amplified into supernormal stimuli, thus producing unprecedented levels of pleasure not previously attainable through the natural environment that our senses evolved within.

Additionally, there are certain emotions that we’ve evolved to express as well as understand simply because they increase our chances of survival within our evolutionary niche, and thus artistic representations of these types of universal human emotions will also likely play a substantial role in our aesthetic preferences.  Even the evolved traits of empathy and sympathy, which are quite advantageous to a social species such as our own (due to them reinforcing cooperation and reciprocal altruism among other benefits), are employed by those that are perceiving and appreciating these artistic expressions.

Another possible evolutionary component related to our appreciation of art has to do with sexual selection.  Often times, particular forms of art are appreciated, not only because of the emotions it evokes in the recipient or person perceiving it, but also when they include clever uses of metaphor, allegory, poetry, and other components that often demonstrate significant levels of intelligence or brilliance in the artist that produced them.  In terms of our evolutionary history, having these kinds of skills and displays of intelligence would be attractive to prospective sexual mates for a number of reasons including the fact that they demonstrate that the artist has a surplus of mental capacity to solve more complex problems that are far beyond those they’d typically encounter day to day.  So this can provide a rather unique way of demonstrating particular aspects of their fitness to survive as well as their abilities to protect any future offspring.

Artistic expression (as well as other displays of intelligence and surplus mental capacity) can be seen as analogous to the male peacock’s large and vibrant tail.  Even though this type of tail increases its chances of being caught by a predator, if it has survived to reproductive age and beyond, it shows the females that the male has a very high fitness despite these odds being stacked against him.  It also shows that the male is fit enough to possess a surplus of resources from its food intake that are continually donated to maintaining that tail.  Beyond this, a higher degree of symmetry in the tail (the visual patterns within each feather, the morphology of each feather, and the uniformity of the feathers as a whole set) demonstrates a lower number of mutations in its genome, thus providing better genes for any future offspring.  Because of all these factors, the female has evolved to find these male attributes attractive.

Similarly, for human beings (both male and female), an intelligent brain that is able to produce brilliant expressions of art (among other feats of intelligence), illustrates that the genome for that individual is likely to have less mutations in it.  This is especially apparent once we realize that the number of genes in our genome that pertain to our brain’s development and function accounts for an entire 50% of our total genome.  So if someone is intelligent, since their highly functional brain was dependent on having a small number of mutations in the portion of their genome pertaining to the brain, this shows that the rest of their genome is also far less likely to have harmful mutations in it (and thus less mutations passed on to future offspring).  Art aside, this kind of sexual selection is actually one prominent theory within evolutionary biology to explain why our brains grew as quickly as they did, and as large as they did.  Quite simply, if larger brains were something that both males and females found sexually attractive (through the feats of intelligence they could produce), they would be sexually selected for, thus leading to higher survival rates for offspring and a runaway effect of unprecedented brain growth.  These aesthetic preferences would then likely carry over to general displays of artistic ability, thus no longer pertaining exclusively to the search for prospective sexual mates, but also to simply enjoy the feats of intelligence themselves regardless of the source.  So there are many interesting facets that pertain to likely influential evolutionary factors relating to the origin of artistic expression (or at least the origin of our mental capacity to do so).

Neuroscience & The Arts

One final aspect I’d like to discuss that pertains to the arts within the context of the sciences, lies in the realm of neuroscience.  As neuroscientists are progressing in terms of mapping the brain’s structure and activity, they are becoming better able to determine what kinds of neurological conditions are correlated with various aspects of our conscious experience, our personality, and our behavior in general.  As for how this relates to the arts, we should also eventually be able to determine why we have have the aesthetic preferences we do, whether they are based on: various neurological predispositions, the emotional tagging of various past experiences via the amygdala (and how the memory of those emotionally tagged experiences change over time), possible differences in individual sensitivities to particular stimuli, etc.

Once we get to this level of understanding of the brain itself, when we combine it with the conjoined efforts of other scientific disciplines such as anthropology, archaeology, evolutionary biology and psychology, etc., and if we collaborate with experts in the arts and humanities themselves, we should definitely be able to answer a plethora of questions relating to the origin of art, how and why it has evolved over time as it has (and how it will likely continue to evolve given that our brains as well as our culture are continually evolving in parallel), how and why the arts affect us as they do, etc.  With this kind of knowledge developing in these fields, we may even one day see artists producing art by utilizing this knowledge in very specific and articulate ways, in order to produce expressions that are the most aesthetically pleasing, the most intellectually stimulating, and the most emotionally powerful that we’ve ever experienced, by design.  I think that by putting all of this knowledge together, we would effectively have a true science of the arts.

The arts have no doubt been a fundamental facet of the human condition, and I’m excited to see us beginning to learn the answers to these truly remarkable questions.  I’m hoping that the arts and the sciences can better collaborate with one another, rather than remain relatively alienated from one another, so that we can maximize the knowledge we gain in order to answer these big questions more effectively.  We may begin to see some truly remarkable changes in how the arts are performed and produced based on this knowledge, and this should only enhance the pleasure and enjoyment that they already bring to us.

Neurological Configuration & the Prospects of an Innate Ontology

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After a brief discussion on another blog pertaining to whether or not humans possess some kind of an innate ontology or other forms of what I would call innate knowledge, I decided to expand on my reply to that blog post.

While I agree that at least most of our knowledge is acquired through learning, specifically through the acquisition and use of memorized patterns of perception (as this is generally how I would define knowledge), I also believe that there are at least some innate forms of knowledge, including some that would likely result from certain aspects of our brain’s innate neurological configuration and implementation strategy.  This proposed form of innate knowledge would seem to bestow a foundation for later acquiring the bulk of our knowledge that is accomplished through learning.  This foundation would perhaps be best described as a fundamental scaffold of our ontology and thus an innate aspect that our continually developing ontology is based on.

My basic contention is that the hierarchical configuration of neuronal connections in our brains is highly analogous to the hierarchical relationships utilized to produce our conceptualization of reality.  In order for us to make sense of the world, our brains seem to fracture reality into many discrete elements, properties, concepts, propositions, etc., which are all connected to each other through various causal relationships or what some might call semantic hierarchies.  So it seems plausible if not likely that the brain is accomplishing a fundamental aspect of our ontology by our utilizing an innate hardware schema that involves neurological branching.

As the evidence in the neurosciences suggests, it certainly appears that our acquisition of knowledge through learning what those discrete elements, properties, concepts, propositions, etc., are, involves synaptogenesis followed by pruning, modifying, and reshaping a hierarchical neurological configuration, in order to end up with a more specific hierarchical neurological arrangement, and one that more accurately correlates with the reality we are interacting with and learning about through our sensory organs.  Since the specific arrangement that eventually forms couldn’t have been entirely coded for in our DNA (due to it’s extremely high level of complexity and information density), it ultimately had to be fine-tuned to this level of complexity after it’s initial pre-sensory configuration developed.  Nevertheless, the DNA sequences that were naturally selected for to produce the highly capable brains of human beings (as opposed to the DNA that guides the formation of the brain of a much less intelligent animal), clearly have encoded increasingly more effective hardware implementation strategies than our evolutionary ancestors.  These naturally selected neurological strategies seem to control what particular types of causal patterns the brain is theoretically capable of recognizing (including some upper limit of complexity), and they also seem to control how the brain stores and organizes these patterns for later use.  So overall, my contention is that these naturally selected strategies in themselves are a type of knowledge, because they seem to provide the very foundation for our initial ontology.

Based on my understanding, after many of the initial activity-independent mechanisms for neural development have occurred in some region of the developing brain such as cellular differentiation, cellular migration, axon guidance, and some amount of synapse formation, then the activity-dependent mechanisms for neuronal development (such as neural activity caused by the sensory organs in the process of learning), finally begin to modify those synapses and axons into a new hierarchical arrangement.  It is especially worth noting that even though much of the synapse formation during neural development is mediated by activity-dependent mechanisms, such as the aforementioned neural activity produced by the sensory organs during perceptual development and learning, there is also spontaneous neural activity forming many of these synapses even before any sensory input is present, thus contributing to the innate neurological configuration (i.e. that which is formed before any sensation or learning has occurred).

Thus, the subsequent hierarchy formed through neural/sensory stimulation via learning appears to begin from a parent hierarchical starting point based on neural developmental processes that are coded for in our DNA as well as synaptogenic mechanisms involving spontaneous pre-sensory neural activity.  So our brain’s innate (i.e. pre-sensory) configuration likely contributes to our making sense of the world by providing a starting point that reflects the fundamental hierarchical nature of reality that all subsequent knowledge is built off of.  In other words, it seems that if our mature conceptualization of reality involves a very specific type of hierarchy, then an innate/pre-sensory hierarchical schema of neurons would be a plausible if not expected physical foundation for it (see Edelman’s Theory of Neuronal Group Selection within this link for more empirical support of these points).

Additionally, if the brain’s wiring has evolved in order to see dimensions of difference in the world (unique sensory/perceptual patterns that is, such as quantity, colors, sounds, tastes, smells, etc.), then it would make sense that the brain can give any particular pattern an identity by having a unique schema of hardware or unique use of said hardware to perceive such a pattern and distinguish it from other patterns.  After the brain does this, the patterns are then arguably organized by the logical absolutes.  For example, if the hardware scheme or process used to detect a particular pattern “A” exists and all other patterns we perceive have or are given their own unique hardware-based identity (i.e. “not-A” a.k.a. B, C, D, etc.), then the brain would effectively be wired such that pattern “A” = pattern “A” (law of identity), any other pattern which we can call “not-A” does not equal pattern “A” (law of non-contradiction), and any pattern must either be “A” or some other pattern even if brand new, which we can also call “not-A” (law of the excluded middle).  So by the brain giving a pattern a physical identity (i.e. a specific type of hardware configuration in our brain that when activated, represents a detection of one specific pattern), our brains effectively produce the logical absolutes by nature of the brain’s innate wiring strategy which it uses to distinguish one pattern from another.  So although it may be true that there can’t be any patterns stored in the brain until after learning begins (through sensory experience), the fact that the DNA-mediated brain wiring strategy inherently involves eventually giving a particular learned pattern a unique neurological hardware identity to distinguish it from other stored patterns, suggests that the logical absolutes themselves are an innate and implicit property of how the brain stores recognized patterns.

In short, if it is true that any and all forms of reasoning as well as the ability to accumulate knowledge simply requires logic and the recognition of causal patterns, and if the brain’s innate neurological configuration schema provides the starting foundation for both, then it would seem reasonable to conclude that the brain has at least some types of innate knowledge.