Wednesday, August 20, 2008

Cosmos ex Natura 5: Holy War against Science

Left: WMAP image of the cosmic background radiation, gives the echo of the cosmic fireball at the point light separated from matter when the plasma of charged particles first coalesced into atoms. It provides evidence that our universe had an explosive beginning, but it doesn't suggest the God created it, nor that this is evidence for 'let there be light'. Right: The biota occupy the cosmic equator through a major central epoch of the universe's evolution and thus form a cosmological manifestation of the interactive culmination of the four forces of nature.

Our idea of the universe and our own relationship with it as biological organisms has been profoundly transformed by the scientific revolution. We now know that the universe has an explosive beginning some 12 billion years ago in which the cosmological processes of the universe at large are complemented by differentiation of the four fundamental wave-particle forces of nature. At the same time we know, despite its relatively fragile nature on the cosmic scale that life is the supreme manifestation of interactive complexity of the four forces of nature on a cosmic footing. Life thus has a unique status in cosmic terms and occurs over an epoch of 3.5 billion years, spanning nearly a third of cosmic history.

The investigative process of science has its basis in the skeptical principle: in which a theory becomes accepted only if it withstands disproof through validation in every natural situation which might refute it, rather than the untested assumptions of spiritual faith, which asserts that belief in God is essential, and lack of faith is betrayal. Affirmative belief has meant that the cherished and often simplified assumptions of religious cosmologies have gone unquestioned for fear of retaliation if not for the simple lack of critical scrutiny.

Sabbatical creation defies the natural order. Although light is created before the stars, consistent with the cosmic background, the plants are impossibly created before the Sun, moon and stars. The firmament of the heavens is "raqiya" a beaten hemispherical bowl, dividing waters above and below, in which the stars are fixed. Earth is a flat domain created by bunching the waters under heaven to one place. Night and day happen before the sun is placed in the heavens. The fishes and whales and the birds are created a day before the land animals and long after the plants.

Ideas that the earth is flat, overlaid by heavens in which the astronomical bodies are set, as if on some gigantic hemispherical ceiling by God have proved to be simply folk myths, fantastic tales having no credibility in the harsh light of careful experiment. Vested religious interests have tried to silence this discovery process, for example endeavoring to excommunicate Galileo for correctly discovering that the Earth orbits around the Sun, rather than being fixed in the centre of the universe, around which all other objects revolve. However these efforts have over time eventually proved in vain because the natural evidence is there for all to see, once we discover how to ask the right question.

Despite the overwhelming detail and consistency of the scientific revolution, which has by the turn of the third millennium unveiled the dynamics of the universe at large, reached the doors of the theory of everything unifying the cosmological forces of nature, unleashed nuclear holocaust, and not only laid bare the genetic code, but decoded the human genome as well, the fact that religion is based on affirmative belief rather than skeptical inquiry has led to a situation of stand-off, where key aspects of the scientific description, such as the genetic evolution of life, continue to be rejected by religious believers, who frequently interpose over the scientific description the same simplistic scriptural accounts.

An attempt to overlay the Sabbatical creation on the inflationary cosmology, based on the WMAP observations being 'let there be light" followed by a dark era before the galaxies formed ignores the manifest inconsistencies and uses the scientific discoveries to retro-fit the six-day creation to observed events - faith interposed over fact. The idea that the sabbatical account is an inspired reflection of a divine intervention seen through a glass darkly millennia before these discoveries raises more questions than it solves.

A key area still to be finally resolved in the lab is the exact path by which life began on Earth. However, far from indicating God made RNA and then DNA to support his life plan, the accumulating evidence indicates that planets are commonplace features of stellar systems and that those in the 'goldilocks zone' where liquid water exists are by no means uncommon. Rather than being an impossible contrivance of vanishing probabilities requiring God to intervene, the molecular precursors of life and of nucleic acids themselves may have an origin in the first gas clouds forming solar systems, and have showered on the early Earth in abundant proportions.

Right: HCN and HCHO form major constituents of gas clouds in star-forming regions of the Orion nebula. Left: HCN is capable of polymerizing in association with other molecules to form both the pyrimidine (U, C) and purine (A, G) bases of nucleic acids. HCHO is likewise capable of generating a variety of sugars including ribose. Above: ATP the monomeric ribonucleotide unit, which forms the archetype of both energy source and structural unit of RNA, along with the other bases G,C and U enabling complementary replication, is a co-pentamer of HCN and HCHO. Both purines and pyrimidines have also been discovered in the Murchison meteorite.

Central to the debate between religion and science is the issue of evolution and whether life is too complex and wonderful to have been crafted by the blind groping of evolution rather than divine creation, or its new guise, 'intelligent design'. Because evolution is a process which happens over relatively long time-scales, Christian fundamentalists have attempted to portray it as merely a conjecture, despite the fact that some evolutionary process are very rapid and genetic sequencing having laid bare the historical record of untold evolutionary transformations, which provide evidence so detailed, that the denial of it forms the dark side of affirmative belief - a holy war against the manifest truth.

By claiming that evolution is simply a theory which has arguments for it and arguments against it creationists falsely imply there is no real experimental confirmation of any of the evolutionary links between species which make the diversity of life a sensible and meaningful system. If the biota were designed by God why are there parasites and diseases, some of which have altogether diabolical manifestations? It is these diseases, from influenza, through HIV to tuberculosis which show the most obvious signs of rapid evolutionary adaption. Why are there carnivorous predators if killing is deemed a sin?

Two arguments typical of the intelligent design advocates are irreducible complexity and specified complexity, both of which manifestly fail the scientific test of skeptical inquiry. Irreducible complexity claims that complex biological systems possess irreducible complexity and could not have evolved because removing any one component makes the whole system fail. This is a fallacy because it is only intelligently designed systems which suffer from this flaw. A living system can arrive at a situation of irreducible complexity by evolution from systems which are not irreducible, either because they have redundancies which are later pruned out by natural selection, or through natural stability structures evolving to become genetically coded irreducible systems. For example key metabolic pathways such as the citric acid cycle are likely to have evolved from natural polycarboxylic acid pools by genetic takeover, resulting in an efficient cycle which later looks irreducible. Other systems touted as evidence for irreducible intelligent design such as the camera eye are clearly not irreducible at all and have obvious evolutionary intermediates.

Left: Naturally occurring eyes show all forms of
intermediate in the formation of the camera eye.

Right: A compound eye on an insect leg elicited
by a mouse gene involved in vertebrate eye development.

The camera eye has often been cited as something that could not have evolved by stages, because its functionality only exists in its completeness of design. However there are diverse examples of pinhole camera pit eyes forming all the intermediate stages of formation of a camera eye. Moreover eyes diverse as the insect compound eye and the vertebrate camera eye use homologous genes to trigger their development, showing that eyes which appear to be founded on radically different principles have a common genetic origin.

Other examples, such as the rotary bacterial flagellum, which might seem to have to be designed in one step entirety can also be easily explained through transfer of functionality from genes which first evolved to fill other roles, as genes making up the rotary assembly have been shown to have sequence homology with related genes having other functions. Thus one of the creative aspects of evolution is its capacity to bring together adventitious combinations of existing or modified genes or gene modules in new integrated functionalities.

Specified complexity is another scientifically false notion that complex structures which are not simply random have to be instructed by a design specification to exist. This is manifestly false and fails to understand critical properties of dynamical chaos and the fractal complexity of structures which emerge from edge of chaos dynamics. Molecular matter is complex largely because of the unique complexity of the way the four forces of nature broke symmetry in the big bang at the origin of the universe. As a result of this symmetry-breaking quarks bind together in threes to form neutrons and protons which in turn bind tightly together to form atomic nuclei with neutral and positive charges, resulting in a complex semi-periodic series of some 100 electrically polarized atoms with orbital electrons capable of forming molecular orbitals and hence chemical bonds.

The capacity for chemical bonding does not stop with the ionic and covalent bonds of ball and stick mechanical molecules, but continues unresolved in a string of weaker cooperative H-bonds, hydrophobic, polar and van der Waal interactions resulting in the complex folding and global cooperativity of large protein and RNA molecules. This process is a quantum fractal and continues in upward scales from molecular complexes, through organelles to cells and finally tissues, organs such as the brain and whole organisms. If the complexity comes from design, it is the design of the forces of nature we need to look at, to understand why tissues are capable of becoming complex when encoded by the genetic information in living evolving organisms.

Living organisms exist as complex structures only because the universe is based on non-linear interaction of the forces of nature. Tissues are fractal molecular structures in a manner similar to the way the non linear dynamics makes the Mandelbrot set arguably the most complex known object in mathematics.

It also needs to be understood that intelligence itself - something possessed by whole brains of intact organisms to aid their survival is not necessarily the best or most fertile basis to generate new viable forms. The entire landscape of life, both in terms of genetic sequences and the folded domains of proteins, consists of modular structures. Higher organism genes are divided into functional subunit exons separated by non-coding introns. This provides not just for random mutations of the code but for functional shuffling of active subdomains to form new combinations. The introns likewise allow for complex RNA-based dynamic modular regulation of whole batteries of genes in ways which can result in new phenotypic and regulatory pathways. Furthermore our genomes are littered with the remains of transposable elements and viruses which in addition to causing deleterious events can facilitate new forms of regulation and horizontally transfer whole genes between species in a way which enables useful genes to find themselves in completely new places where their effects can combine in new ways. Indeed the evidence is now becoming clearer that the tree of life of higher organism evolution emerged from a tangled web in which genes are freely passed between species enabling life to exist in almost any extreme environment. There is also manifest evidence that the genomes of higher organisms have arisen from multiple symbiotic events bringing together diverse metabolic systems.

What is almost entirely misunderstood by the intelligent design movement is that far from being random mutation, evolution, is the most rapid generator of complex form in the universe because it is a massively parallel quantum molecular computer based on parallel nucleic acid replication. It can't be reasonably compared to any naive probability process based on random processes, because the extreme degree of parallel exploration of the space of possibilities makes genetic algorithms the most efficient computational process in the universe. For all its elegant structure, and even consciousness, even super-intelligent design is cumbersome, clunky and completely unsuited to generate new life forms.

Supporters of intelligent design suffer from a delusion that emergence and evolution of life are somehow beyond the scope of natural explanation, but they fail to properly apply their theories to rigorous test. The central arena for the viability of such a hypothesis is development of the organism, not evolution, or the origin of life, for it is in development that we can see biological design in action and arriving at a precise result over time scales we can readily observe, both in the lab, and out in the millpond.

The evolution of intelligent design illustrated in the Buick emblem: The intelligent designer creates each individual de-novo, having only the same general concept. Because there is an external designer following his own predilection, there is no absolute requirement for a new design to depend in any significant way on the form of the predecessor. Both development and evolution are fundamentally a product of the designer only and not the design itself. In successive generations, one Buick shield can become three and then an Eagle. By contrast natural evolutionary change leaves the fingerprint of its variation in the genomes of the ancestors and their descendants. Corporations, operating systems, and technological innovation all follow the 'evolutionary' protocols of intelligent design.

The central model for intelligent design is the watchmaker - that is human craftsmanship of an elegant precision applied on small scales to produce a complex yet stable mechanism. By extrapolation, we are then expected to believe that God, given his much more awesome mysterious powers, could by the same process of design, external to the blind groping of nature, produce something so elegant and complex as a living organism.

The trouble with this idea is that external design works from the top down and the only really complex machines humanity has been able to construct are digital computers, which, while they are capable of delivering a lot of challenge and entertainment, are founded on one very basic notion, that of a Von Neumann architectured Turing machine. There is no mystery of life or consciousness here. All the responses available are fully described by the simple instruction set.

Robotic car assembly illustrates development by intelligent design. The parts above have no capacity for interactive self-assembly, because the process has to be entirely guided by the external intelligent design process. The process of development is instead driven externally on a global basis by robotic machines executing the intelligent design algorithm, or by God as the case may be!

By contrast, development, from the ovum to the organism, is based on mutual interaction resulting in sequential differentiation and depends on quantum processes such as protein folding which are intractable as classical computational processes. Embryonic development, while ultimately determined at the molecular level by the DNA code, is an emergent interactive process, both resulting in changes at the intracellular level, as cell types specialize, and inter-cellular transformation, in the sequence of interactions between individual cells, and cell layers.

Moreover, development reflects the underlying evolutionary process which made it possible, as shown below. Furthermore evolutionary changes are sequentially dependent in the information possessed by the organism, rather than an external intelligent designer. They are clearly dependent on small transformations of an existing genomic instruction set, so the genetic information of the organism is the key instructor of the process under small discrete changes caused by mutation and rearrangement. By contrast intelligent design is liable to abrupt change, as illustrated in the Buick example, and even when there is a degree of homology, is is merely a conceptual reworking rather than a topological bifurcation.

Left-center: Formation of the neural tube, after gastrulation has already invaginated ectoderm and endoderm, is a self-interactive topological bifurcation. Right: Development of the eye recapitulates the essential bifurcations of the evolutionary process which generated it.

There is absolutely nothing about this process which suggests an external intelligent designer, but rather an internal self-interactive process. This goes all the way to the central nervous system, where there are massive migrations of cells on pre-developed scaffolds in response to growth factor signals expressed by other specific target cell types, as well as massive cell and synapse death to prune the connections to those which are required for effective sentient function.

We thus see that even in the developmental context, where we clearly have an encoded biological design and a process which is elegantly targeted to a specific outcome, there is no hint of a designer except the interaction between the DNA sequence and maternal cytoplasmic inheritance. To suggest that the DNA sequence is God given, rather than a result of mutability of the process due to the occasional errors of replication resulting from the impossibility of absolute perfection, the interaction of transposable genetic elements and the modular nature of genes and their intervening non-coding sequences now known to have a major role in gene regulation is frankly pissing in the wind.

Relationships between evolution and development: Early embryonic forms of vertebrates all have the long tails and many segments of fishes because they have a deep underlying evolutionary relationship, in which fishes became land animals. The program of development is encoded in our DNA and the evolutionary process reflects the long-term transformations of his program's form and function. Neither development, nor evolution show any of the traits of intelligent design. Both do show the traits of autonomous variation.

The final knell for the intelligent design hypothesis is the human genome project and with it the genome projects of related and other species, which lay bare the encoding of the evolutionary process and bring it right up to date in real time during the cultural divergence of human groups in the cultural epoch.

Above: Genetic tree of evolutionary divergence between chimps neanderthals and humans confirms each evolved from a common ancestor - the bane of creationists and 'intelligent designers'. Below: Evolutionary tree of Human ethnic groups using a variety of different analyses of genetic sequences gives a consistent overall evolutionary tree for human societies with minor variations due to the differing effects of sexual recombination and other process on the types of DNA change analysed. The inevitable conclusion is that humanity is evolving in real time as we speak.

The critical gap still existing in the scientific description of reality is the central question of how the brain evokes subjective consciousness. Since religious descriptions, in dealing with a God outside and/or above the mortal coil of the physical universe and involve themselves in questions of the afterlife beyond physical death, religions are predominantly descriptions from a conscious sentient perspective, in which the biological and physical aspects of reality are frequently shunned, as part of an inferior, bestial, or degraded condition.

Science thus badly needs to make some progress into the depths of how the brain generates subjective consciousness to avoid being accused of being a purely materialistic description of no real weight in deciding the lofty questions of the fate of sentient existence.

Deborah Kelemen has found that the tendency to favour explanations invoking purpose-seeking yet false explanations of natural phenomena - promiscuous teleology - is shared by both religious and non-religious adults, suggesting that humans are neurobiologically predisposed to be susceptible to 'intelligent design' and creationist explanations (Cognition (DOI: 10.1016/j.cognition.2009.01.001, Callaway, Ewen "Humans may be primed to believe in creation" New Scientist 2 Mar 2009).

Intelligent design closes in on the designer:
Four views of artificial intelligence (internet)

Coming from the diametrically opposite pole to affirmative belief, there is a purely materialistic claim of intelligent design, applied, not by the religious, but by those who follow a purely mechanistic, cyborg line, in which the human brain is pictured as just another form of computer. In an act of reverse faith, this belief is that artificial intelligence will provide the complete solution to how the brain makes sense of the world. In this description, the notion of subjective consciousness is discarded as a superfluous, non-objective, non-scientific idea, having no replicable correlates on which we can base real experimental evidence, because subjective experience is not an objective verifiable phenomenon at all. The artificial intelligence approach presents another form of intelligent design, for it claims that the only defining characteristics of the brain are its computational structure and function and that, once this is elucidated, there is nothing more to discover.

However, artificial intelligence has proved incapable of making the huge strides it promised. An interesting example is optical character recognition, one which computers should really be able to handle, where scanned snippets of old texts called Captchas (Completely Automated Public Turing test to tell Computers and Humans Apart) are used to make sure real humans log onto web sites, eliminating phishing and spamming computers, which are still unable to perform unambiguous character recognition, despite decades of AI research into such areas.

The brain is in no way like a digital computer and uses completely different principles, involving waves of excitation, chaotic dynamics, continuous, rather than entirely discrete digital communication, and probably, into the bargain, exotic quantum phenomena. Despite having 10^11 neurons and 10^15 synapses, the brain is an extraordinarily bad numerical calculator, having a digit span of only about 7. Cultures exist with no linguistic terms for number and there is debate whether there are any hard-wired skills for numeracy in the human brain. Moreover the sorts of problems the conscious brain is best able to solve - anticipating immediate and serious threats to survival in the open environment - are notoriously intractable computational problems which would leave a digital computer being eaten by its tyrannosaurus equivalent because it became catatonic at the crossroads and took too long to compute whether to jump out of the way of the predator.

Top row: Localization of pitch, melody and rhythm perception in music.
Left: Different aspects of language function result in activity in varying regions of the cerebral cortex. Center: Visual processing for color and motion is done separately in parallel. Right: Ocular dominance of one or other eye is distributed dynamically across the visual cortex and varies as a result of cortical plasticity. In blind people these regions may be used for spatial representation using auditory sensation rather than vision. Lower left: Processing in the olfactory cortex distinguishes two odors through global 'holographic' differences in the wave form of the excitation. Lower right: Brain excitations are broad frequency chaotic excitations. Rather than discrete processing, the brain appears to use phase coherence as in a hologram to distinguish the relevant stimuli from the random groundswell of noise.

Neuroscience is beginning to uncover intriguing relationships between how different areas of the cerebral cortex handle sensory and cognitive processes and the subjective consciousness with which they are associated. For example different regions process colour and motion, resulting in pathologies, in which people who have had injuries in particular regions, cannot experience either colour or motion, instead witnessing a grey landscape or a confusing sequence of frozen stills when the coffee is poured. Likewise rhythm, melody and pitch in music, and semantic meaning and articulate expression in language, are processed in distinct regions. Moreover, the allocation of such functionality is capable of plasticity, so that in blind people, visual regions may be involved in auditory spatial processing.

Furthermore, the brain does not depend on digital processing. Although long axons are pulse-coded, sending a spike train at a rate corresponding to the intensity of the stimulus, other neurons have continuous potential changes. Neuron-neuron connections are not entirely electrical, with many different types of chemical neurotransmitters involved, some of which can have profound effects on consciousness. Memory likewise has a major biochemical component involved in delayed recall. The neuron as a cell is far from a trivial discrete component like a transistor or a simple additive unit, with large pyramidal cells having many different types of excitatory and inhibitory synapses and up to 10,000 synaptic connections, many of which are capable of non-linear interactions, resulting in complex dynamics between neurons.

The global nature of brain waves is broad-spectrum, rather than simple resonances, allowing for transitions in and out of chaos, and using holographic type principles of wave phase correlation, to distinguish the critical information being paid attention to from the groundswell of noise. Some researchers also suggest that quantum phenomena may play a role in brain function and that there may be a relationship between quantum uncertainty and quantum entanglement, and the capacity of the conscious brain to anticipate circumstances and possess the attribute of free-will.

Conscious states of the brain do not appear to be associated with any specific brain centre, but rather a function of the higher levels processes distributed over the entire cerebral cortex. Although the conscious brain remains the abyss in the scientific description, brain science is bringing us ever-closer to an understanding and challenging our assumptions, both religious and mechanistic.

In the next section we will explore how the scientific description for morality, might alter our view of morality and spirituality and how it might help us come to terms with a more sustainable paradigm of human participation in safeguarding the future of life on Earth.

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