The ID Report

Robert Deyes
ARN Correspondent

The Spanish Paseos Por La Naturaleza (A Walk Through Nature) series continues with a review of Biologic Institute researcher Douglas Axe's thesis on the probabilistic barriers that make a neo-Darwinian explanation for the origin of protein folds untenable. Given his scientific background, Axe is well qualified to argue against the undirected origin of protein structure and convincingly counters those who extravagate over the much-heralded modular transfer of folds between proteins.

The Paseos Por La Naturaleza series aims to further strengthen the global influence that the Intelligent Design movement already enjoys and raise awareness of important academic resources that are today challenging orthodox Darwinism and revitalizing the call for a fresh perspective on scientific discourse.

The fifth installment can be found at:

Como los pliegues proteinicos derrumban el edificio neo-darwinista (see also darwinodi.com)

A Review Of The Case Against A Darwinian Origin Of Protein Folds By Douglas Axe, Bio-Complexity, Issue 1, pp. 1-12

By Robert Deyes
ARN Correspondent

Proteins adopt a higher order structure (eg: alpha helices and beta sheets) that define their functional domains. Years ago Michael Denton and Craig Marshall reviewed this higher structural order in proteins and proposed that protein folding patterns could be classified into a finite number of discrete families whose construction might be constrained by a set of underlying natural laws (1). In his latest critique Biologic Institute molecular biologist Douglas Axe has raised the ever-pertinent question of whether Darwinian evolution can adequately explain the origins of protein structure folds given the vast search space of possible protein sequence combinations that exist for moderately large proteins, say 300 amino acids in length. To begin Axe introduces his readers to the sampling problem. That is, given the postulated maximum number of distinct physical events that could have occurred since the universe began (10exp150) we cannot surmise that evolution has had enough time to find the 10exp390 possible amino-acid combinations of a 300 amino acid long protein.

The battle cry often heard in response to this apparently insurmountable barricade is that even though probabilistic resources would not allow a blind search to stumble upon any given protein sequence, the chances of finding a particular protein function might be considerably better. Countering such a facile dismissal of reality, we find that proteins must meet very stringent sequence requirements if a given function is to be attained. And size is important. We find that enzymes, for example, are large in comparison to their substrates. Protein structuralists have demonstrably asserted that size is crucial for assuring the stability of protein architecture.

Axe has raised the bar of the discussion by pointing out that very often enzyme catalytic functions depend on more that just their core active sites. In fact enzymes almost invariably contain regions that prep, channel and orient their substrates, as well as a multiplicity of co-factors, in readiness for catalysis. Carbamoyl Phosphate Synthetase (CPS) and the Proton Translocating Synthase (PTS) stand out as favorites amongst molecular biologists for showing how enzyme complexes are capable of simultaneously coordinating such processes. Overall each of these complexes contains 1400-2000 amino acid residues distributed amongst several proteins all of which are required for activity.

Axe employs a relatively straightforward mathematical rationale for assessing the plausibility of finding novel protein functions through a Darwinian search. Using bacteria as his model system (chosen because of their relatively large population sizes) he shows how a culture of 10exp10 bacteria passing through 10exp4 generations per year over five billion years would produce a maximum of 5×10exp23 novel genotypes. This number represents the 'upper bound' on the number of new protein sequences since many of the differences in genotype would not generate "distinctly new proteins". Extending this further, novel protein functions requiring a 300 amino acid sequence (20exp300 possible sequences) could theoretically be achieved in 10exp366 different ways (20exp300/5×10exp23).

Ultimately we find that proteins do not tolerate this extraordinary level of "sequence indifference". High profile mutagenesis experiments of beta lactamases and bacterial ribonucleases have shown that functionality is decisively eradicated when a mere 10% of amino-acids are substituted in conservative regions of these proteins. A more in-depth breakdown of data from a beta lactamase domain and the enzyme chorismate mutase has further reinforced the pronouncement that very few protein sequences can actually perform a desired function; so few in fact that they are "far too rare to be found by random sampling".

But Axe's landslide evaluation does not end here. He further considers the possibility that disparate protein functions might share similar amino-acid identities and that therefore the jump between functions in sequence space might be realistically achievable through random searches. Sequence alignment studies between different protein domains do not support such an exit to the sampling problem. While the identification of a single amino acid conformational switch has been heralded in the peer-review literature as a convincing example of how changes in folding can occur with minimal adjustments to sequence, what we find is that the resulting conformational variants are unstable at physiological temperatures. Moreover such a change has only been achieved in vitro and most probably does not meet the rigorous demands for functionality that play out in a true biological context. What we also find is that there are 21 other amino-acid substitutions that must be in place before the conformational switch is observed.

Axe closes his compendious dismantling of protein evolution by exposing the shortcomings of modular assembly models that purport to explain the origin of new protein folds. The highly cooperative nature of structural folds in any given protein means that stable structures tend to form all at once at the domain (tertiary structure) level rather that at the fold (secondary structure) level of the protein. Context is everything. Indeed experiments have held up the assertion that binding interfaces between different forms of secondary structure are sequence dependent (ie: non-generic). Consequently a much anticipated "modular transportability of folds" between proteins is highly unlikely.

Metaphors are everything in scientific argumentation. And Axe's story of a random search for gem stones dispersed across a vast multi-level desert serves him well for illustrating the improbabilities of a Darwinian search for novel folds. Axe's own experience has shown that reticence towards accepting his probabilistic argument stems not from some non-scientific point of departure in what he has to say but from deeply held prejudices against the end point that naturally follows. Rather than a house of cards crumbling on slippery foundations, the case against the neo-Darwinian explanation is an edifice built on a firm substratum of scientific authenticity. So much so that critics of those who, like Axe, have stood firm in promulgating their case, better take note.

Read Axe's paper at: http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1

Further Reading

Michael Denton, Craig Marshall (2001), Laws of form revisited, Nature Volume 410, p.417

By Robert Deyes
ARN Correspondent

In 2001 Stephen Meyer, Paul Nelson and Paul Chien wrote a lengthy discourse that explored the scientific challenges that the Cambrian Explosion of life poses to the Darwinian account of animal origins (1). Central to their arguments was the idea that biological processes in the organismic context are so tightly integrated that changes in one process invariably require compensatory changes elsewhere (1). Their illustration of this basic premise seemed intuitive enough:

"If an engineer modifies the length of the piston rods in an internal combustion engine, but does not modify the crankshaft accordingly, the engine won't start. Similarly, processes of development are so tightly integrated temporally and spatially that one change early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream" (1)

Drawing from examples cited in the biological literature and comments made by opinion leaders, notably geneticist John McDonald and zoologist Soren Lovtrup, the verdict they arrived at was that "those genes which govern major changes, the very stuff of macroevolution, apparently do not vary, or vary only to the detriment of the organism" (1).

In an effort to model the tight integration of biological processes my sons and I teamed up to assemble a functional multi-component machine better known as the K'Nex Drop-N-Swing. Not only did we successfully demonstrate how the operability of the 'Drop-N-Swing' mechanism was dependent upon the components having precisely the spatial dimensions that they display but we also showed how adjustments to any one of these required concordant adjustments elsewhere in the machine.

The layout of the Drop-N-Swing resembles the sky drop and swing carousel rides one finds in modern amusement parks (see http://www.youtube.com/watch?v=udr-RxcnUFU). On one side a centrally-located motor drives a series of four sequential gears each of which has just enough gear teeth to crank a chain-linked chair lift up a two foot-tall tower. Because a defined portion of the circumference of the largest gear lacks teeth and can therefore not crank up any weight, the chair drops down immediately upon reaching the top of the tower. This 'rise and fall' cycle is made possible through 86 chain links that form a closed chain circuit around two sprockets located at the bottom and top of the tower. The bottom sprocket is connected to the gear system that consequently turns the chain and causes it to lift up the chair.

As my sons toyed around with the Drop-N-Swing they found that they were unable to decrease the chain length and tower height without cutting down on the number of gear teeth. That is, if they were to maintain the rise and fall capabilities of the chair lift, concordant adjustments were needed at more than one location (otherwise the chair would get irreversibly stuck on the top sprocket). Even the tower height could not be facilely altered since the repeating unit of the tower struts did not correspond to an integral number of chain links.

Newsworthy cases in biology testify to the underlying charge brought by Meyer et al that major evo-morphing of structure and anatomy could not have been brought about through random piecemeal changes to already-extant body plans. Famously Nobel Prize winning biologist Ed Lewis elucidated crucial details about the genetics of embryonic patterning in fruit flies (2-4). Focusing on a group of genes known collectively amongst drosophila geneticists as the Bithorax Complex, Lewis built on the pioneering work of his predecessors who had identified homeotic (developmental patterning) mutants in the Bithorax gene that produced insects with an extra pair of wings (2-4). These appeared appended to the front portion of sophisticated flight balance-mediating organs called halteres situated on either side of the flies (2-4). The Bithorax mutant broke thorassic segment identities (ie one segment was replaced by another). But most importantly the mutant larva died early in development (2).

Meyer et al note how this additional wing pair "innovation" was viably unsustainable for the largely self evident reason that "the developmental mutation was not accompanied by the many other coordinated developmental changes that would have been necessary to ensure the production of the appropriate muscles at the appropriate place on the fly's body" (1). Renowned Cambridge developmental biologist Peter Lawrence made his position clear in a review of the overall findings of homeotic mutation research:

"Homeotic mutations are encouraging because they raise the clarifying prospect of a class of controlling genes responsible for large chunks of the body pattern. They also impress because the mutations produce massive anatomical transformations; it was even thought such mutations could allow the sudden generation of new animal groups during evolution - an idea that looks increasingly implausible (individuals produced by such mutations are very unfit!)." (4)

One cannot help but acknowledge the futility of a story that claims that evolution could have brought about beneficial large scale changes to body plan architecture. The evidence speaks for itself. And simple attempts at modeling do nothing less than support the science.

Further Reading
1. Stephen C. Meyer, Paul A. Nelson, and Paul Chien (2001) The Cambrian Explosion: Biology's Big Bang, See http://www.discovery.org/articleFiles/PDFs/Cambrian.pdf, p.36, This article also appears in the peer-reviewed volume Darwinism, Design, and Public Education published with Michigan State University Press

2. Vidyanand Nanjundiah (1996) The 1995 Nobel Prize in Physiology or Medicine, Resonance, http://www.ias.ac.in/resonance/Mar1996/pdf/Mar1996ResearchNews.pdf

3. Stephen Jay Gould (2002) The Structure of Evolutionary Theory, The Belknap Press of Harvard University Press Cambridge, Massachusetts, p.1096

4. Peter Lawrence (1992), The Making of a Fly: The Genetics Of Animal Design, Blackwell Scientific Publications, London, p.211

By Robert Deyes
ARN Correspondent

"Depending on the type of grammar used in forming a given sentence, the brain will activate a certain set of regions to process it, like a carpenter digging through a toolbox to pick a group of tools to accomplish the various basic components that comprise a complex task" (1). This was the descriptive offered by one review on how it is that diverse regions of the human brain are recruited to tease out the meaning of sentences when we communicate with each other (1). Cutting edge research into brain function, using American Sign Language as a platform, has unpacked the detail of exactly how the brain achieves this split-second feat (1,2).

In sign language messages can be expressed in one of two ways. As with English, 'signers' can use ordered words to convey their message (eg: John gives his lunch to Mary). But they can also move their hands in a manner that specifically relays concepts and ideas- what linguists call inflection(2). In languages such as German and French inflections are easily identifiable as suffixes that can be tagged onto the ends of words to denote, amongst other things, the case or the gender of the word or the 'role' that a subject or object in a sentence plays in a given interaction (John giving lunch to Mary in the above example) (2). But sign language, notes Rochester University psychologist Aaron Newman offers "a unique opportunity to directly contrast these two means of marking grammatical roles within the same language" (2).

Newman employed functional Magnetic Resonance Imaging (fMRI) to zero in on the spatial-temporal brain activities that accompany both word order and inflection-based communication. What he uncovered was nothing short of remarkable. There exists a network of brain regions including the dorsolateral prefrontal cortex (DLPC), the superior and posterior temporal sulcus (STS), the caudate nucleus, the middle temporal gyrus (MTG), the angular gyrus (AG) and the left inferior frontal gyrus (IFG) that are operative during both the interpretation of word order and inflection processing (2). Importantly significant differences exist in the "relative weighting" of activation in these regions depending upon which of these two modes of message transmission is being called upon (2). The DLPC and the right hemisphere AG are more dominantly active when word order-critical sentences are put in front of us. In contrast the MTG and the posterior STS are more active during inflection processing (2). The overarching conclusion borne out by the results of this study is that "specific parts of the neurocognitive system recruited for grammatical processing are dependent on the type of information that must be processed" (2).

Over the years my interest in language and brain function has been fueled by my own exposure to cultures outside of those of my native England. I grew up speaking Portuguese, Spanish and to a lesser extent French. Unlike English, these and other Romantic languages display a requirement for word inflection in both verb endings and noun genders. Whereas English leans towards compound verb usage, Portuguese, Spanish and French show complex verb endings (e.g., The English phrase I shall come translates into Portuguese as Eu virei). When I traveled this month to the Brazilian Society of Biochemistry meeting in Foz de Iguassu in southern Brazil, I was relieved to find that I could slip almost effortlessly into both the written and spoken forms of Portuguese. It was a joy to find that, despite the odd non-conformity, my Portuguese had remained unadulterated over the years. Little did I know that I was employing cognitive functions that differed from those that I use in my more usual English setting.

On the flight back I settled down to read about the work of one Evelina Fedorenko who as an MIT psychologist has played an instrumental role in deciphering the functional hotspots of linguistic cognition (3). Her research has concentrated on mapping the 'within language' specificity (linguistic processing cognition) and 'domain' specificity (non-linguistic cognition) areas of the brain (3). Fedorenko and her close colleague Nancy Kanwisher have devised a localizer task approach for studying brain function (3). By asking individual subjects to perform cognitive tasks that place demands on localized regions of the brain (eg: contrasting pronounceable non-words like florp with real words like flop), they have been able to identify those regions that "engage in retrieving the meanings of individual lexical items and in combining these lexical-level meanings into larger meaning structures" (3).

Once back at home I had the chance to ask my father - a linguist by training - for his take on Newman's and Fedorenko's work. His principle observation was that sign language could only serve as a model for written words. Whereas sign language is sequential, spoken forms of language are multi-layered with sounds, grammar, vocabulary, intonation and gesture all acting together to achieve the conveyance of information. But what was plainly obvious to both of us was that through its sheer processing speed, the cerebral linguistic toolbox had no equivalent in anything that a carpenter might find on his workbench. Almost two decades ago brain biologist John Eccles noted that our linguistic capacity was pivotal in ensuring that we became the dominant species on our planet (4). The latest research is confirming Eccles' assessment. And the brain architecture associated with language processing is turning out to be mind-bogglingly complex.

So, what of the evolution of language usage in humans? Perusing through the literature one finds a story that invariably begins with the need for some form of communication amongst early hominids. Having given up the safety of arboreal living in favor of an expansive conquest of terra firma, these hominids, we are told, would have relied on each other for information on the whereabouts of food, shelter and predatory dangers and may have been endowed with the simple descriptive function of language (4). "Cladistic branching with a great genetic change" accompanied the rise of Homo habilis, considered by many as the 'initiator' of spoken language (4). Great genetic advances gave us Homo erectus and finally Homo sapiens sapiens with his expressive, descriptive and argumentative capabilities (4). We are led to the idea that even this climactic achievement was accessible to the un-shepherded roving of natural selection (4).

Of course nothing in this story remotely addresses the question of how the interplay of diverse regions of the brain, such as that which we see above, became so firmly entrenched into the very fabric of how we communicate. The literature is silent about the details. As the twentieth century linguist Noam Chomsky argued language is "a skill that human beings are innately predisposed to acquire" (5). Today evolutionists are hard pressed to come up with an account for the origin of such an innate predisposition. At its core, the cerebral linguistic toolbox is a phenomenon that blows the mind and sabotages the evolutionist's dream of a viable account for the origin of a vital part of our humanity.

References

1. Aaron Blank (2010) Sign Language Study Shows Multiple Brain Regions Wired for Language, See http://www.rochester.edu/news/show.php?id=3610

2. Newman AJ, Supalla T, Hauser P, Newport EL, & Bavelier D (2010) Dissociating neural subsystems for grammar by contrasting word order and inflection, Proceedings of the National Academy of Sciences of the United States of America, 107 (16), 7539-44 PMID: 20368422

3. Evelina Fedorenko, Functional localization in fMRI studies of language, See http://www.mit.edu/evelina9/www/funcloc.html

4. John Eccles (1991) Evolution Of the Brain, Creation Of The Self, Routledge Press, London, pp.95-96

5. Steve Blinkhorn (2003) Language Instinct, in The Science Book, ed. Peter Tallack, Weidenfeld And Nicolson Publishers, London, pp. 386-387

Review Of Chapter 13 Of Signature In The Cell, by Stephen Meyer, HarperOne Publishers, ISBN: 9780061894206

By Robert Deyes
ARN Correspondent

I never would have suspected that the literary sensation Dr Seuss' The Cat In The Hat Comes Back would be used to make a point about the devastating shortcomings of origin of life theories (1). But when I read one of the later chapters of Meyer's Signature In The Cell which in one foul swoop discredited Hermann Muller's fortuitous origins of DNA, Henry Quastler's DNA self replication hypothesis and Manfred Eigen's ideas on hypercycles I could not help but be fascinated by his use of this children's classic in his exposition. Of course in their own unique ways each of these scientists became steadfastly convinced that they were onto something of great significance that would lead to fruitful avenues on the all important question of how life had begun.

Muller drew inferences from his own work on viruses, in particular bacteriophages ('bacteria eaters'), equating these simple organisms to "a gene that copies itself within the cell" (2). He envisioned these as being somehow analogous to primitive DNA floating around in the chemical-rich soup of the early earth (2). Quastler on the other hand suggested that polynucleotides could act as templates for replication through complementary base pairing (3). And Eigen chose to assume that 'self-reproducing molecular systems' involving RNA molecules and basic enzymes could somehow supply an early form of transcription and translation, later forming hypercycles that would have preceded the arrival of the earliest cells (4).

So how is the Cat in the Hat relevant? Crucial aspects of the above mechanistic propositions, writes Meyer, parallel the antics of our feline friend as he unwillingly redistributes the mess he has created in the house of his none-too-happy hosts. Origin of life scientists have similarly been trying for decades to "clean up the problem of explaining the origin of [biological] information" only to find that they have "simply transferred the problem elsewhere- either by presupposing some other unexplained sources of information or by overlooking the indispensable role of an intelligence" (1). And their modern day brethren, with the apparent sophistication of computer-housed evolutionary algorithms, have fared little better. Meyer's unpacking of the reality behind Ev, for example, described by its author Thomas Schneider as "a simple computer program" that attempts to evolve the information content of DNA binding sites in a hypothetical genome, is a case in point (5). In Ev Schneider specifies the sequence of these DNA binding sites and incorporates the code for the binding site 'recognizer' (protein) into the genome (5). The relative penalties for mis-binding or non-binding of the recognizer to sequences are pre-set into the program (5).

Ev stands guilty as charged since, as Meyer asserts, it presupposes an unexplained source of information (1). And for that matter so does the much-celebrated evolutionary algorithm Me Thinks It Is Like A Weasel. "[Both] succeed in generating the information they seek" writes Meyer "either by providing information about the desired outcome from the onset, or by adding information incrementally during the computer program's search for the target". The so-called 'active information' imparted by the programmer allowed both programs to assess the proximity of any given sequence to a pre-specified target- hardly a fair representation of the Darwinian mechanism in action.

I had the opportunity to hear Michigan State University philosopher Robert Pennock present on another much-touted algorithm called AVIDA during the 2008 Bioethics Forum in Madison, Wisconsin. The forum carried the promissory title Evolution In The 21st Century. And Pennock certainly did his utmost to adopt the 'Darwin immortalized' slant that the event was promoting (6). From the deliberations that followed Pennock's exposition it appeared on the surface that AVIDA trumped its predecessors by not pre-specifying any sort of evolutionary target (5). But as I found out on further inspection appearances can be deceptive. In fact the AVIDA world is home to a brood of digital organisms that are rewarded with resources and replicate each time they perform logic functions (eg: AND, OR). Meyer's principle criticism is that the inherent complexity of these functions in no way equates to that which we find in genes and therefore unreasonably "diminishes the probabilistic task that nature would face in "trying" to evolve the first reproducing cell".

The problems with AVIDA run deeper still as Winston Ewert, William Dembski and Robert Marks II have made all too clear in their expository dissection of digital organisms. They conclude that "AVIDA generates active information from a number of knowledge sources provided by the programmer and, with respect to an evolutionary strategy, performs poorly with respect to other search strategies using the same prior knowledge" (7). In fact AVIDA organisms are endowed with virtual genomes and the capacity to replicate and operate within a realm of assigned merit values for each of the logic functions they perform (6).

More generally, the thrust of Meyer's attack has everything to do with the law of conservation of information (COI) (6). COI theory supplies us with a critical insight: "all computer search algorithms of moderate to high difficulty require active information" (ie from the programmer) and "the amount of information in a computer in its initial state equals or exceeds the amount of information in its final state" (1). That is, evolutionary algorithms do not furnish us with a means by which to simulate the origin of genetic information through natural selection given that too much information is siphoned into these algorithms from the onset by external intelligence.

For the same reasons already mentioned, the mess left by Dr Seuss' Cat in the Hat is once again proverbially pertinent to the matter at hand. In this regard, Meyer is to be congratulated for his divulgence of biology's foremost skeleton in the closet- the absence of a scientifically plausible explanation for the origin of biological information. On that matter, we should embrace his enthusiasm for change in the way that clenched-fist biologists filter debate over their view of life's unfolding story.

References

1.Stephen Meyer (2009) Signature In The Cell: DNA And The Evidence For Intelligent Design, HarperOne Publishers, pp. 271-295

2.Iris Fry (2006) The origins of research into the origins of life, Endeavour, Volume 30, Issue 1, March 2006, pp. 24-28

3.Robert L. Herrmann (1975) Implications of Molecular Biology for Creation and Evolution, JASA 27 (December 1975): pp. 156-159, http://www.asa3.org/ASA/PSCF/1975/JASA12-75Herrmann.html

4.Vladimir Red'ko (1998) Hypercycles, Principia Cybernetica, See http://pespmc1.vub.ac.be/HYPERC.html

5.Thomas Schneider (2000) Evolution of biological information, Nucleic Acids Research, 2000, Vol 28, pp. 2794-2799

6.Robert Deyes (2008) AVIDA As A 'Teleo-LOGIC' Model Of Life, Access Research Network, See http://www.arn.org/blogs/index.php/2/2008/08/09/avida_as_a_teleo_logic_model_of_life

7.Winston Ewert, William Dembski, Robert Marks II (2009) Evolutionary Synthesis Of Nand Logic: Dissecting A Digital Organism, Proceedings Of The 2009 IEEE International Conference On Systems, Man, And Cybernetics, San Antonio, Texas, USA (October 2009), pp. 3047-3053, See http://evoinfo.org/papers/2009_EvolutionarySynthesis.pdf

By Robet Deyes
ARN Correspondent

If we were to think of the height of the Eiffel tower as representing the age of our earth then the existence of humanity would be nothing more that the skin of paint on the pinnacle knob. This was the opening perspective offered by Professor of Philosophy Sean Kelly whose inaugural lecture at this year's Annual International Bioethics Forum on the science of consciousness kick started a series of talks by a preeminent cast of academic thinkers and speakers. Kelly's ensuing factual inventory set the tone for others to follow. During their brief history, humans have become a force that has incontrovertibly impacted our planet. 95% of that skin of paint of human existence occurred before the advent of agriculture. And during that time humans have shown that they are the only beings with a capacity not only for complex language but also for storing information outside of themselves in the form of books and multimedia. No other species dwells upon historical time like we do. University of Minnesota ethnopharmacologist Dennis McKenna, who spoke immediately after Kelly's 'opener', concurred. Complex language, he noted, depends on synesthesia-style relationships between spoken words and a corresponding set of symbols that imbue our daily experiences with meaning. When this phenomenon emerged no one knows for sure although the deepest historical evidence to-date, that of the Blombos Cave in South Africa, suggests that it may have existed as early as 75,000 years ago.

University of Wisconsin cognitive scientist Antoine Lutz later presented his summarization of Rene Descartes' Dualistic theory as part of his much-awaited talk. And his delivery of the historicity of cognitive philosophy was received with rapturous applause by an expecting audience. Descartes considered the pineal gland in the brain to be the center of integration of both the body and the non-material mind. Modern science has of course dismissed Descartes' vision of this much-trumpeted 'seat of the soul' by showing the brain to be a highly distributed system of separate functions and reciprocal connectivities. In fact the 'global work space' of the human brain is made of 10exp9 neurons with 10,000 connections. Current neuro-imaging techniques provide a very approximate sketch of this work space which is thought to perform thousands of neurological processes every second. With all of its neuroplasticity, the brain is evidentially built to change in response to experiences. Hot off the press in the Proceedings Of The National Academy Of Sciences this week is a paper outlining how the brain acts "like a carpenter digging through a toolbox to pick a group of tools to accomplish the various basic components that comprise a complex task" (1,2) (Although I would add at a rate several orders of magnitude faster than any carpenter could ever hope to reach).

Throughout this year's forum there was a noticeable disquiet over how best to define consciousness in terminology that could be assimilated into a scientific framework. Historically Immanuel Kant was the first to argue rationally that the human mind puts forward 'categories of understanding' that define how we view the cosmos. Over a century later the German philosopher Karl Jaspers wrote of the Axial age- a 400 year period of grand synchronicity when philosophers and sages across the globe pondered over the existence of transcendent meaning and spirituality in our world. Forum speaker Sean Kelly chose to talk about consciousness as the permeable boundary that separate us from our surroundings while British author Peter Russell focused on the inherent self-awareness that characterizes consciousness in humans and, to a much lesser extent, monkeys and dolphins. During the panel discussions some merely posited that consciousness inevitably emerges as an evolutionary phenomenon. Of course this latter end-point does nothing to satisfy the explanation-ravenous appetites of the truly scientifically-minded. We may rightly ask why evolution would produce conscious beings that are able to engage in religious experiences?

Functional MRI and contemporary biochemistry are telling us a lot about brain function and providing foundations for understanding at least the molecular facets of consciousness. Purdue University Distinguished Chair of Medicinal Chemistry Robert Nichols took the forum rostrum in earnest and supplied us with a compendious examination of how the brain thalamus processes our senses and gates information that is then sent to columns of pyramidal cells in the frontal cortex. A region of the brain known as the Locus Coeruleus acts as a 'novelty detector' that focuses our attention at any given moment to the events happening around us. We can now map out regions of the brain involved in sensory gating by using a class of compounds called entheogens such as psilocybin that act on serotonin 5HT2A receptors in the frontal cortex. Entheogens also shut down that Raphe region of the brain stem which during our 'awake' hours is rapidly firing electrical impulses and selectively releasing serotonin. Entheogens, noted Nichols, break the mental framework and therefore help the brain to temporarily live 'outside the box'. Some Silicon Valley scientists are rumored to have used similar compounds to achieve new heights of innovative thought.

How have entheogens further aided consciousness research? Johns Hopkins behavioral biologist and Bioethics Forum speaker Roland Griffiths has used psilocybin in his own attempts to mimic mystical experiences. In 1962 Harvard psychiatrist Walter Pahnke performed his famous 'Good Friday' experiment from which he concluded that psilocybin occasioned mystical mimetic experiences. Griffiths revisited Pahnke's work in an investigation involving 37 test subjects who were in one sense or another involved in religious practices. Interestingly all individuals reported experiencing feelings of awe, peace, and ineffable joy. 70% of these test subjects reported that the ingestion of Psilocybin had given them one of the top five most memorable and positive moments of their lives. Psilocybin treatment leads to a preferential processing of positive emotional expression (eg: happy faces) and therefore presents a therapeutic avenue for treating clinical depression.

In 1964, Eric Kant became the first to use entheogens to treat depression in advanced-cancer patients. Later Pahnke showed that these same compounds could be used to improve the psychological outlook for the terminally ill. More recently Franz Vollenweider, the serving Director of the Heffter Research Centre for Consciousness Studies in Switzerland, documented some of the altered states of consciousness (ASCs) that subjects have described as part of his own pioneering experiments. Descriptives such as oceanic self boundlessness, oneness and unity with the universe form part of the eleven ASC dimensions that are commonly found in the associated peer-reviewed literature. Vollenweider's presentation at the forum was perhaps the most data-rich of all showing, amongst other things, how the intensity of ASCs is significantly affected by underlying personality traits.

At a fundamental level consciousness is a phenomenon that is deeply mysterious and to-date has escaped even the most concerted attempts at a simple explanation. According to Peter Russell we are in the throes of a revolution in thought not unlike that which caused the rejection of Ptolomeic epicycles during the Copernican era. The meta-paradigm that exists in science today views the world as one that is fully explainable through recourse to space, time and matter. And yet, notes Russell, this meta-paradigm of materialism through which we are epicycling in no way predicts the advent of conscious beings such as ourselves. Truth be told Russell's own brand of pan-psychism, a doctrine that holds that even the atom is in some lesser degree conscious of itself, is little more than a fanciful cerebration with a materialistic flavor. Thankfully there have been formidable intellectual resistances against it.

Further Reading
1. Sign Language Study Shows Multiple Brain Regions Wired For Language, Science Daily, April 30th, 2010

2. A.J.Newman, t. Supalla, P. Hauser, E.L. Newport, D. Bravelier (2010) Dissociating Neural Subsystems For Grammar By Contrasting Word Order And Inflection, Proceedings Of The National Academy Of Sciences, Vol 107, p. 7539

Full details of seminars and presenters who attended the 9th Annual International Bioethics Forum:
Taking the Measure of the Magic Mirror, held on April 22-23, 2010 can be found at: http://www.btci.org/

Review Of Probability's Nature And Nature's Probability - Lite, by Donald Johnson
ISBN: 978-0-9823554-4-2

By Robert Deyes
ARN Correspondent

Zoologist Richard Dawkins has historically used the concept of 'junk DNA'- those apparently useless portions of genomes- to lead the charge against the creationists' position of purpose in nature. His view on the matter is quite simple: "creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA". In light of what we now know about DNA, Dawkins' should spend some earnest time reviewing whether his littered genomes are so littered after all. In fact the term 'junk DNA' is now seen by many an expert as somewhat of a misnomer since much of what was originally categorized as such has turned out to be pivotal for DNA stability and the regulation of gene expression. In his book Nature's Probability And Probability's Nature author Donald Johnson has done us all a service by bringing these points to the fore. He further notes that since junk DNA would put an unnecessary energetic burden on cells during the process of replication, it stands to reason that it would more likely be eliminated through selective pressures. That is, if the Darwinian account of life is to be believed. "It would make sense" Johnson writes "that those useless nucleotides would be removed from the genome long before they had a chance to form something with a selective advantage....there would be no advantage in directing energy to useless structures".

Johnson's seemingly unstoppable siege on Darwinian orthodoxy is both well researched and freshly captivating. At the risk of unjustly losing credibility, several distinguished scientists have carried the baton of dissent against the received wisdom of modern day Darwinists. Those who have stayed abreast of the Intelligent Design (ID) claims need no reminding of the powerful arguments presented in their own counter-offensive, particularly regarding the fossil record. Johnson's recapitulation of the Cambrian explosion and the trilobite high acuity visual system at the base of the Cambrian leave the reader wondering why the inclusion of ID has in recent years been so fiercely opposed by those in the biological sciences who carry reputational clout.

It turns out that much of the 'science' buttressing the anti-ID rhetoric is supportive of the very position it claims to counter- that of intelligent design. Computer simulations and genetic algorithms that purport to simulate the process of evolution do nothing of the sort, slipping in acts of intelligent agency at every turn. Summarizing the status quo, Johnson notes for example how AVIDA uses "an unrealistically small genome, an unrealistically high mutation rate, unrealistic protection of replication instructions, unrealistic energy rewards and no capability for graceful function degradation. It allows for arbitrary experimenter-specified selective advantages". Not faring any better, the ME THINKS IT IS LIKE A WEASEL algorithm is programmed to direct a sequence of letters towards a pre-specified target.

One never tires of reading about the irreducible complexity of the multi-component bacterial flagellum. And Johnson does not disappoint in his engaging overview of this showpiece of ID theory. The icing on the irreducible complexity "cake" appears in his further consideration of sexual reproduction and the integrated aspect of DNA and protein synthesis. The plethora of symbiotic relationships we find throughout nature also form part of Johnson's inventory of examples as he moves the reader decisively to the conclusion that natural processes cannot generate novel genetic information.

What is the price we pay for refusing to bring ID into the science arena? Johnson's summarization of philosopher of science Del Ratzch's answer to this question is a call to rally: "any imposed policy of naturalism in science has the potential not only of eroding any self-correcting capability of science but of preventing science from reaching certain truths". Johnson condemns those who refuse to evaluate the merits of scientific evidence on the basis of philosophical or theological commitments. Indeed the compatibility of ID with differing theological views does not negate the scientific validity of its arguments. "Obviously, ID proponents have the freedom of religion allowed by the country of residence" notes Johnson "but those beliefs should not detract from the scientific evidence".

As Johnson details, the duplicity in standards of the anti-ID lobby was made plain in the charges brought against molecular biologist Richard Sternberg who was removed from office as editor of the Proceedings Of The Biological Society Of Washington after publishing an ID-friendly paper authored by philosopher Stephen Meyer even though Sternberg had faithfully followed the journal's regulations for publication. Cases such as this show that while ID theorists are heavily criticized for not having peer-reviewed publications to support their position they and their entourage are vehemently censured whenever they do attempt to meet their critics' demands. Johnson draws from an extensive list of quotes from reputable scientists and philosophers who have made known their dis-satisfaction with the blind beliefs of Darwinian ideology. The 'knowledge stopper' that is naturalistic evolution has today handcuffed these same scientists to the pillars of 'majority rule' even though invigorating alternatives such as those that invoke intelligent design meet the strictest demands for scientific rigor.

In the last chapter of his book Johnson reviews not only the probabilistic evidence in support of ID but also the uniformitarian nature of ID's conclusions. Occam's razor, neatly summarized by the mantra "The simplest solution is the best" provides us with a fruitful avenue for deciding which theories on the origins and existence of life should be open for discussion. Since many would argue that ID wins the Occam challenge, we can safely conclude that its rejection stems not from its lack of scientific merit but from underlying philosophical prejudices. As with all scientific theories, that of ID remains falsifiable. Johnson concedes that there is no privileged status that somehow locks ID away from disputation. Indeed if natural processes can be shown to produce the fine-tuning of the universe, the origin of life from non-life, the rich diversity of living forms that appeared in the Cambrian and the increasing information-based complexity of life throughout our earth's history, then the 'necessity of design' will have been given its marching orders. But until then ID theory can only serve to enrich the scientific landscape.

PART I: Experimental Foundations

The plans had been made, details finalized and all expenses paid. I was to travel to the south coast of England to complete my training for the British Sub-Aqua Club Sports Diver certificate. I boarded a train from London's Waterloo station down to the quiet seaside resort of Bournemouth where I was received by relatives. For the next two weeks I commuted to the nearby harbor town of Poole and headed out on a rigid hull inflatable boat with five other students to complete a series of required dives. The testosterone-induced camaraderie soon brought us together into a close-knit group. We were assigned our respective diving 'buddies'- a practice that is almost a mandatory requirement of amateur sport diving. We quickly picked up on the diving lingo and were Hi-fiving our way to the end of each day.

All of our sorties out to sea went according to plan. That is, until the final afternoon. As we were heading back to the safety of the mooring station the weather took a turn for the worst. Surging waves reduced visibility to little more than a few feet and with the quickly darkening skies we knew we were in trouble. In desperation the pilot of the boat radioed for help. Minutes later we were spotted by the coastal 'cavalry guard'- a British Navy Sea King helicopter equipped with all the fittings that one might expect for a major rescue operation. Fortunately the terrifying experience of being stranded out at sea ended without further incident. We were escorted to the calmer waters of a local bay from which we headed home for a feast of fried fish served in greasy, vinegar-sodden newspaper (the quintessentially English supper). That same evening we all reconvened to mull over the events as they had unfolded. We bonded socially knowing that, in the midst of our differences, there was at least one thread of commonality by which we could all relate to each other. We were all now sports divers with a story to tell.

A craving for social connection is a deeply-rooted aspect of the human psyche (1). So much so that even at the cellular level there are key molecular markers associated with the subjective feeling of social isolation (loneliness). Just three years ago a seminal study using a microarray based approach identified some of the genes that are differentially expressed in the immune cells of individuals who struggle with subjective social isolation (2). The 'transcriptional fingerprint of loneliness' that came about as a result provided researchers with a window into how negative feelings over social experiences can adversely impact our health. Most importantly a total of 209 transcripts, representing 144 genes, were found to be differentially expressed in the leukocytes of subjectively lonely individuals (2).

Over-expressed genes included transcription factors and chromatin structure regulators involved in leukocyte proliferation and immune activation while under-expressed genes were predominantly those of cell-cycle inhibitors (2). A crucial piece of the loneliness puzzle was the discovery of reduced glucocorticoid receptor-mediated transcriptional activity. Other signaling pathways involving the Oct and CREB/ATF transcription factor families were also significantly affected (2). From a disease standpoint the results were in close agreement with clinical findings that correlate subjective loneliness with an increased risk of inflammation-mediated disease and decreased resistance to viral infection (2).

Functional Magnetic Resonance Imaging (fMRI) techniques have supplemented these molecular studies by showing how areas that are active in the brain during moments of physical pain are also active during prolonged periods of social exclusion (3,4). In one experiment participants were subjected to MRI scanning of brain blood flow while interacting with virtual team mates in a computer ball-throwing game aptly named Cyberball (3,4). Participants became emotionally distressed whenever they were excluded from activities in the virtual environment (3,4). Two areas of the brain that register and regulate physical pain- the prefrontal and the anterior cingulate cortex- were shown to play a decisive role in the ensuing emotional distress circuit (3,4). In close agreement with this study, a recent review by UCLA psychologists Matthew Lieberman and Naomi Eisenberger made plain how our response to emotional stresses and pleasures relies on the same neurological processes that register negative and positive physical sensations (5).

Pharmaceutical intervention is gaining traction as one of several possible therapeutic avenues for treating loneliness. Psychobiologist Jaak Panksepp has suggested that the use of opioids or naturally occurring regulators of separation distress such as oxytocin or prolactin might reverse feelings of social isolation (3). In their award-winning book Loneliness: Human Nature And The Need For Social Connection cognitive neuroscientist John Cacioppo and former editor of Harvard University Press William Patrick offer a more pro-active method which involves a change in one's own thought patterns and perceptions (6). Their highly acclaimed EASE way of social connection (E= Extend Yourself, A= Action Plan, S= Selection and E= Expectation) builds on years of research carried out at the Center of Cognitive Science at the University of Chicago (6). Central to their rationale is the counterintuitive principle that in order to get around the 'passive coping' that characterizes the inertia of loneliness, we must make ourselves available to meet the needs of others. Such an assessment runs against the tide of sentiments that pervade our culture. But Cacioppo and Patrick are ever-emphatic about what their experience has shown:

"The most difficult conceptual hurdle for people in the throes of loneliness is that, although they are going through something that feels like a hole in the center of their being- a hunger that needs to be fed- this 'hunger' can never be satisfied by a focus on 'eating'. What's required is to step outside the pain of our own situation long enough to "feed others"...We are told in childhood to share and to 'do unto others' It sounds simplistic, like a Sunday school lesson. It doesn't sound like behavior that fits into the adult, workaday world. Certainly it does not sound like advice based on hard science. And therefore this wisdom, which should be a principle to guide us, we dismiss as a cliche. As a result, we get caught up in our problems and the confusion of our tortured perceptions and we don't practice what we know to be wise and true...Real change begins with doing, and what may seem like silly reminders may be exactly what it takes to get us to do what needs to be done, in the moment, every day" (6).

The 'integrative intelligence' that allows us to read social cues is severely impaired whenever loneliness strikes. The end result is that we build inaccurate impressions of our human interactions- a phenomenon that neuroscientists have termed 'loss of executive control' (7). In such cases, it is the brain's frontal lobes that incorrectly regulate our judgment of the external world (7). When my wife and I boarded a flight out of Heathrow airport on the 26th of February, 2001 with only a one-way ticket to the United States we knew that we were taking a risk by ripping ourselves out of a firm bedrock of friends and family to begin life in unfamiliar territory. And for the first months we felt the negative impact of living outside the social scene. But by applying the 'tried and tested' wisdom of modern psychology we were able to pull ourselves back into a medium within which we could feel comfortable again. In short, we rediscovered our sense of being human.

In Part II I will examine the sweeping evolutionary suppositions that often accompany this otherwise-fruitful area of research into the human social condition.

Literature Cited

1. Dan Russell (1996) The UCLA Loneliness Scale (Version 3): Reliability, validity, and factor structure, Journal of Personality Assessment, 66, 20-40.

2. Steve W Cole et al (2007) Social Regulation Of Gene Expression In Human Leukocytes, Genome Biology, 8, R189.

3. Jaak Panksepp (2003) Feeling the Pain Of Social Loss, Science, 302, pp. 237-239.

4. Naomi Eisenberger et al (2007) Does Rejection Hurt? An fMRI Study Of Social Exclusion, Science, 302, pp.290-292.

5. Matthew Lieberman and Naomi Eisenberger (2009) Pains And Pleasures Of Social Life, Science, 323, pp.890-891.

6. John Cacioppo and William Patrick (2008) Loneliness: Human Nature And The Need For Social Connection, Norton Publishers, New York, NY, pp. 233-243.

7. Ibid, p.35

Robert Deyes
ARN Correspondent

The Spanish Paseos Por La Naturaleza (A Walk Through Nature) series continues with an examination of the atheistic brand of religion that pervades the scientism movement. The neo-atheist Peter Atkins has been one of the modern day crusaders of this movement with his scathing allegation that science presents the only reliable means by which to understand nature and the world around us. Many are those who today revolt against such a position.

The Paseos Por La Naturaleza series aims to further strengthen the global influence that the Intelligent Design movement already enjoys and raise awareness of important academic resources that are today challenging orthodox Darwinism and revitalizing the call for a fresh perspective on scientific discourse.

The fourth installment can be found at:
Lanzando los "huevos podridos" del cientismo fuera del sarten(See also OIACDI)

Review Of Probability's Nature And Nature's Probability - Lite, by Donald Johnson
ISBN: 978-0-9823554-4-2

By Robert Deyes
ARN Correspondent

PART I
If Intelligent Design is to be escorted out of science debating halls because of its compatibility with a belief in a deity, undirected naturalism should likewise be excluded on the premise that it is the core tenet of nontheistic religions like Atheism.. Such is the opening message of the `Lite' version of a book whose title Probability's Nature And Nature's Probability is so captivatingly simple that one cannot help but take at least a cursory look through its pages. And the author Donald Johnson has an impressive list of scientific accolades to his credit brought about by a passion for (and not a disdain of) science- a PhD in chemistry from Michigan State University, ten years as a senior research scientist in the medical and scientific instrumentation field, a twenty year college-teaching career and a second PhD in Computer Science.

Johnson's personal reflections reveal a lot about how he came to espouse the views of the Intelligent Design movement. Over the course of his career, Johnson grew increasingly skeptical over natural causation as applies to the origin of life. Science as we know it, he notes, should make testable predictions. While speculation does have a place in science, it needs to be presented as such and not dressed up and served up as a `platter of facts' for consumption by a public unaccustomed to the nuances of scientific argumentation. Johnson brings to the fore the blatant misrepresentations of what is truly `probable', `plausible' and `feasible' in the context of origins of life research as he takes the reader on a whirlwind tour of mathematical notation and probabilistic reasoning.

Theories that are at loggerheads with the singular origin of our universe can in most cases be soundly discredited on the grounds that they lack empirical evidence and testability. The oscillating (Big Bang/Big Crunch) model in particular is easily pushed aside given a notable absence of data in support of a universe that will reach the critical density needed to cause its collapse. For an infinite-existence model we are confronted with the question of how a system that has reached maximum entropy over infinite time could ever give rise to a non-maximum entropy cosmos. In the words of Johnson "an infinitely old universe would be energy dead with no capacity for work, since one result of the second law of thermodynamics is that perpetual motion machines are impossible (zero probability)". Other attempts to eschew the extraordinary fine tuning of our universe, such as we see in the manifold iterations of String theory, posit the existence of multiple universes. The metaphysicality of such alternatives however, given that we cannot possibly hope to see beyond the horizon of our own cosmic abode, renders them unqualifiable as real science.

What are we to make of the abundance of life on our planet? As Johnson so clearly conveys, an acceptable definition of life naturally entails a consideration of observable phenomena such as metabolism, growth and reproduction. At the heart of life lies a myriad of proteins that perform critical functions all of which depend on the tight specification of highly-restricted amino acid sequences. Proteins in the ribosome are themselves translated by the very machinery of which they form a part. The DNA that supplies the instructions for their manufacture is a digital code of the highest order with alternative splicing and sequence overlap of the estimated 20-25,000 genes that exist in humans producing somewhere in the order of 100-200,000 distinct proteins.

Even one of the smallest organisms, Mycoplasma genitalium, sports 482 genes although estimates suggest that as few as 151 genes might be all that is needed to make the simplest life form. How might chemical evolution have taken the first baby steps on the road to what one might tentatively call a primitive cell? The reality as Johnson so emphatically hammers home is that science remains clueless over this singularly important question. Since proteins and nucleic acids have long been known to act as an integrated co-operative whole, models that assume a gradual evolutionary process are today considered woefully inadequate for explaining the origins of life. Truth be told, there exists a pervasive 'science as we don't know it' element in everything from RNA world hypotheses to panspermia and the host of proposed undirected natural processes that invoke the role of minerals in early biocatalysis.

With matter and information representing two distinct "domains of existence", biologists are at a loss to explain the origin of the digital code contained in genetic material. DNA carries a large degree of so-called traditional information which provides meaning for subsequent interpretation by the translation machinery. Trevors and Abel wrote how the codons of DNA represent "functional meaning only when the individual amino acids they prescribe are linked together in a certain order using a different language". This has to be one of the outstanding revelations of the bioinformatics revolution. In fact, using his exhaustive knowledge of information science, Johnson demonstrates the extraordinary parallels between a computer program's algorithmic language and the genetic information system contained within every living cell.

What is most impressive about Johnson's text is the breadth and diversity of scientific sources that he draws from. Even those who are heavily committed to undirected naturalism display an apparently unavoidable tendency to use a language that connotes design. So it is that while Darwin's heavyweights seem intent on embracing chance and natural selection as the only drivers of biological change, they are also perhaps unwittingly navigating towards intelligent design through their own corridors of reason.

Further Reading
Trevors, J.T.; Abel, D.L. Chance and necessity do not explain the origin of life. Cell Biol. Internat. 2004, 28, 729-739.