By Robert Deyes
Put intuition aside for a moment and imagine a scenario where E.coli knockout strains that have been deleted for conditionally essential genes are rescued by proteins taken from a protein library composed of >10exp6 de novo designed sequences. The prevailing assumption- that functional proteins are constrained to a very small subset of possible sequences- would lead us to infer that finding them by a random search through sequence space would be tantamount to impossible. But a PLOS One paper published in early 2011 appears on the surface to have given us much room for thought. Scientists from Princeton's Department of Chemistry and Molecular Biology used a combinatorial library of 102-residue long proteins to rescue non-viable E.coli knockouts. The functional losses in the knockout strains affected serine, glutamate and isoleucine biosynthesis and disabled the cells' natural capacity for iron acquisition in iron-limited environments.
The E.coli knockouts were auxotrophic meaning that they exhibited a failure to grow on minimal (M9-glucose) media even after several weeks of incubation. But following transformation with the combinatorial library, several cases of successful colony growth were documented suggesting that the certain genes contained therein had successfully complemented the deletions. Sequence comparisons through formal BLAST searches showed that the rescue proteins involved, eighteen in all, were unlike any protein found in nature.
Truth be told these rescue proteins were not entirely random. Their sequences had been engineered to ensure that they would fold into a stable 3-D structure. And not just any structure. Molecular biologists are well aware that canonical sequence rules exist that must be adhered to if they are to maximize the chances of proteins folding correctly. In an alpha-helical fold, for example, polar and non-polar residues must be carefully ordered to make certain that the hydrophilic ('water-loving') and hydrophobic ('water-hating') faces of the fold emerge. The Princeton group adopted a binary code strategy of polar and non-polar residues to get 1.5x10exp6 four-helix bundles. In this singularly fundamental aspect they were designed.
What was the molecular basis that allowed rescue? From their own experiments the Princeton group ruled out the likely hood that novel pathways that bypass the adverse effects of the knockout genes had arisen since E.coli mutants that were deficient in other steps of the naturally occurring biosynthetic pathways could not be rescued. Also dismissed was the interpretation that "global alterations in metabolism had been induced by the mere expression of foreign genes" (a stress response of some kind) since none of the eighteen rescue proteins appeared to have been unfolded- a tell-tale symptom of such a global response. Mutations that minimally disrupted their structure abolished their rescue capabilities.
The evidence seemed compelling. These de novo sequences were exerting specific fonctional effects that served to avert an otherwise fatal outcome for their bacterial hosts. Still the 'design' point-of-departure raised above was without question central to this particular success story. In his book Signature In The Cell Stephen Meyer has noted how it is sequence specificity that ensures that amino acid chains fold into "useful shapes or conformations" (Ref 1). Without a library tailored for the formation of four-helix bundles, the Princeton study is unlikely to have yielded anything that would come close to salvaging the debilitated bacteria. To make matters worse, this study failed to consider in detail the cooperativity that so evidently characterizes the organismic molecular scheme. What we see here is akin to taking one piece out of a jigsaw puzzle and finding another to put in its place albeit with some considerable force of fit. Those who espouse blind evolution are still left reeling over how to explain the origin of the entire puzzle.
Importantly cells transformed with rescue proteins exhibited growth that was "significantly slower than those expressing the natural protein" (the non-knockout strains). Exponential growth occurred 24-144 hours later and reached culture densities that in some cases were as low as 12-15% of wild-type. The authors readily admit that the library proteins may "function by different mechanisms than the natural proteins they replace". Indeed assays designed to test for the deleted functions failed to show that the de novo sequences exhibited comparable enzymatic activities. The evolutionary inference given by the authors- that billions of years of evolution have driven optimal activities for faster growth- therefore appears to be nothing more than a rehash of a positively stale Darwinian fairytale. After all, if the proteins function by different mechanisms, one cannot allege that they are in any sense on the way to becoming the more efficient naturally occurring protein entities we observe in E.coli today.
For the full PLOS One article see:
Michael A. Fisher, Kara L. McKinley, Luke H. Bradley, Sara R. Viola, Michael H. Hecht (2011) De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth, See http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015364
1. Stephen Meyer (2009) Signature In The Cell: DNA And The Evidence For Intelligent Design, Harper Collins Publishers, New York, p.99
By Robert Deyes
In his 1987 seminal work entitled Impossibility In Medicine the American psychiatrist Jean Goodwin presented to the world the following acutely insightful vista of the brain:
"Despite many assertions to the contrary, the brain is not "like a computer". Yes, the brain has many electrical connections, just like a computer. But at each point in a computer only a binary decision can be made- yes or no, on or off, 0 or 1. Each point in the brain, each brain cell, contains all the genetic information necessary to reproduce the entire organism. A brain cell is not a switch. It has a memory; it can be subtle. Each brain cell is like a computer. The brain is like a hundred billion computers all connected together. It is impossible to understand because it is too complex. As Emerson Pugh wrote, "If the human brain was so simple that we could understand it, we would be so simple that we couldn't."" (1)
In so doing he hinted at an aspect of the brain that tied in well with a philosophical thought-chain expounded by ID philosopher Bill Dembski in his book No Free Lunch:
"Humans have designed all sorts of engineering marvels, everything from Cray supercomputers to Gothic cathedrals. But that means, if we are to believe Melvin Kooner, that a blind evolutionary process...cobbled together human neuro-anatomy which in turn gave rise to human consciousness, which in turn produces artifacts like supercomputers which in turn are not cobbled together at all but instead are carefully designed. Out pop purpose, intelligence, and design from a process that started with no purpose, intelligence, or design. This is magic" (2)
In my most recent essay Lessons From A Broken Brain I provide a high-level overview of key medical moments that helped define the hundred-billion-computer organ housed atop our bodies. The design inference shines through in the brief details I present.
On a somewhat related note there is a fascinating clip on the work of Dutch kinetic sculptor Theo Jansen who has created his own brand of beach creatures. With over twenty years of arduous work under his belt, Jansen started by pulling his 'offspring creatures' up into the wind, then gave them propellers and wings/sails to increase their running power. The commentator on this clip notes that: "through hours of experimenting and trial and error, Theo's designs are becoming more and more independent".
Jansen's own conclusion?
"What I have found about this experience of making new forms of life is that you discover all the problems that the real creator must have had creating this world"
And these are not even thinking, autonomous, reproducing beings! See Beach Creatures
1. No Way: The Nature of the Impossible, edited by Philip Davis and David Park. Cited in Inside The Mind Of God- Images And Words Of Inner Space, edited by Michael Reagan, Templeton Foundation Press, New York, p.61
2. William Dembski (2002) No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence, Rowman & Littlefield Publishers, Inc, Lanham, Maryland, p.369
By Robert Deyes
Shattered assumptions, broken rules and overturned beliefs. The science media seems eager these days to emphasize science's capacity to shift paradigms. And it was such a handful of descriptives that was used to convey the implications of a new study that redefines our view of genome architecture (1). At the heart of such excitement lay a tunicate organism called Oikopleura dioica that carries in its genetic armory "several peculiarities" (1). Weighing in with its 70 million base pairs of DNA Oikopleura is today venerated as the animal with the smallest known genome (1). But what stands out for biologists who have dedicated years to unpacking Oikopleura's treasure box genome is the 'odd ball' physical location of many of its genes (1). The Scientist's Megan Scudellari remarked that "Oikopleura's genes appear to have been shuffled like a deck of cards" (1).
At the apex of this presumed shuffling is that all-elusive but much loved patch-all process called evolution. "UV rays and other mutagens" that bombard Oikopleura as it ekes out its existence just below the ocean surface are the suggested deck dealers of this particular shuffle (1). But apart from this rather misty association between cause and effect, there is precious little in the evolutionary inferences of this study to satisfy an appetite for robust scientific argumentation. To be fair, there are observable facts that we can latch onto and embrace as the products of rigorous science:
(i) Oikopleura's genome is extremely small containing the same number of genes found in humans (18,000) but compacted into a genome that is 1/40th of the size (1). Genome compactness is reflected in small intergenic distances (53% are less than 1Kb)(2).
(ii) While the Oikopleura external phenotype is clearly in line with that observed in other tunicates, the intronic organization of its genome is vastly different (introns are very small peaking at 47 base pairs in length)(2).
(iii) Oikopleura is unique amongst the tunicates in having both male and female individuals (2).
(iv) Oikopleura exhibits high mutation rates and low dN/dS ratios per each 4-day long generation (dN and dS being the rate of substitutions in non-silent and silent sites respectively)(2).
But there is also fact-less guesswork. For example, since this new study found that many of Oikopleura's introns display high sequence homology, the follow-on assertion put forth by the authors is that introns multiplied in the genome in a hap stance, 'by chance' fashion and that genome architecture across the animal kingdom is therefore inherently plastic and unconnected to morphological/developmental complexity (1,2). Such a grossly overstated endpoint does not appear to be supported by anything close to a thorough examination of intron location and animal morphological variability.
Twenty years ago scientists began to understand the intimate role that introns play in gene regulation in higher order animals (3). We now know that intron splicing involves "the precise deletion of an intron from the primary transcript" so that exons on either end can be joined in readiness for protein translation (4). The choice of specific splice sites depends on the surrounding sequence and structure of the RNA (5). Three types of sequence- the 5' splice site, the 3' splice site and a branchpoint sequence- are almost invariably found in pre-mRNA introns of higher eukaryotes although these elements alone are insufficient to account for the specificity of the splicing reaction (5). Additional signals in abutting exons not only ensure that accurate splicing is maintained but also prevent exon 'skipping', which would of course adversely impact the functionality of the translated product (6).
In some cases more than one mRNA can be coded for by a "single stretch of DNA" as a result of different splicing pathways, different intron cleavage sites and selectively active promoters (3). The mouse salivary amylase gene is perhaps the archetypal example of the multi-variant role that introns play in gene regulation. In this instance alternative but nevertheless nucleotide-specific splice sites are used depending upon whether expression is required in salivary glands or the liver (3). Stephen Meyer writes: "like Russian dolls stored within Russian dolls, exons and introns encode multiple genetic messages within themselves and are themselves part of a larger genetic message" (7).
Genomic mapping has shown that "of 5589 introns mapped by interspecies protein alignments, 76% had positions unique to Oikopleura" (2). It is therefore assumed evolutionarily speaking that Oikopleura's single major spliceosome made up of U1 snRNP and U2AF proteins is capable of recognizing donor and acceptor sites in the genome and shuffling introns around accordingly (2). Such a proposed transposition and propagation seems to fly in the face of what we know about the contextual requirements of intron splicing as outlined above. For instance, if differing intron splicing pathways are active in distinct parts of an organism then we would expect their transposition to novel genome sites to be extremely disruptive to gene function within their new context.
Evolutionists' intron-splicing magic is rife with factless guesswork. Even the briefest of considerations as is offered here makes that plain.
1. Megan Sculellari (2010) Who Needs Structure Anyway? The Scientist, 18th November, 2010, See http://www.the-scientist.com/news/display/57814/
2. France Denoeud et al (2010) Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate, Science, Vol 330, pp.1381-1385
3. Benjamin Lewin (1990), Genes IV, Oxford Cell Press, pp.484-486
4. Christopher Wills (1991) Exons, Introns & Talking Genes: The Science Behind The Human Genome Project, Oxford University Press, Oxford UK, p.112
5. Adrian Kramer & Tom Maniatis (1990) RNA Splicing, in Transcription And Splicing, Eds B.D. Hames & D.M. Glover, IRL Press, Washington DC, pp.141-145
6. Ibid. p.159
7. Stephen Meyer (2009) Signature In The Cell: DNA And The Evidence For Intelligent Design, Harper Collins Publishers, New York, p.463
By Robert Deyes
Buried in the most recent scientific literature there is a story of love, sex, and intrigue that has all the makings of a hearty Mills & Boon novel. The central characters of this plot are not lovers wrapped in each others arms but fruit flies that choose their sexual partners according to the microbiota that line their guts (1,2). Lactobacillus plantarum is the 'cupid gut bug' that seems to have greatest influence on sexual preferences (1,2) And it appears to do so by influencing the release of a class of Drosophila pherormones known as cuticular hydrocarbons (1,2). For evolutionists this finding is cited as one possible avenue through which speciation might take place in Drosophila (1,2). For those of us who are critical of such work however there exists one small but important catch. That is that the sexual preferences observed are easily eradicated by simply treating fruit flies that have been raised on different diets, with antibiotics (1,2). In other words, no genetic changes that would ensure irreversible reproductive isolation, and hence speciation, have taken place.
The late paleontologist Stephen Jay Gould was convinced that for speciation to occur, so-called peripheral populations would simply have to become 'locked up'- isolated from the gene flow of their larger ancestral stocks- in such a way that new adaptations would become stable and not watered down by interbreeding (3). Gould's close colleague Niles Eldredge posited that new species could form, "by the mere accumulation of genetic differences in the two segments of a single ancestral species" on the basis of some sort of hypothetical, (however slight) change in the reproductive system (4, p.116). As he went on to add, "some modification of the reproductive system is required for speciation to occur" (4, p. 121).
Unfortunately for Gould and Eldredge such an exit glossed over key mechanistic questions. After all what mechanism could we come up with that ensured irreversible reproductive isolation from ancestral stocks? Attempts to correlate speciation events with some sort of unguided change in the genetic makeup of an isolated population have proved largely unfruitful. In their studies on fruit flies Laura Reed and Therese Markow suggest that reduced sperm motility as well as sperm storage, recovery from storage, or ability to penetrate the micropyle might play an important role in the hybrid incompatibility that results from interspecial crossings (5). But they readily admit that the lack of a known genetic causality for speciation today represents "a major challenge to evolutionary biology" (5). They further add that "no study has yet characterized levels of naturally occurring variation for factors causing postzygotic isolation in any animal taxon" (5). Such a challenge is of fundamental importance if, as Darwin did, evolutionary biologists are to confidently claim that speciation is merely an extension of population variation.
Today some scientists have posited that a small number of genes in individual species might somehow maintain populations as reproductively isolated units. Biologist Daniel Barbash and his colleagues from Cornell University put forward a gene called "Hybrid Male Rescue" (hmr) as a possible candidate speciation gene in fruit flies (6,7). They demonstrated that hmr was responsible for hybrid incompatibility between different species, seemingly acting in concert with an unknown autosomal factor (7). Yet they also recognized that the 13% interspecial amino acid divergence observed in the HMR DNA Binding protein was a tall order for "relaxed selective constraints" to have achieved on their own (7). According to their statistical analysis of mutational frequencies and in line with the Dobzhansky-Muller (D-M) speciation model, they were adamant that some sort of positive selection must have been at work although they were unable to suggest what selective pressures might have acted to favor reproductive isolation (6,7).
Darwin himself recognized that whatever factors might be involved in ensuring reproductive isolation they could not have arisen through natural selection. He wrote in The Origin of Species that "the sterility of species when first crossed, and that of their hybrid offspring, cannot have been acquired...by the preservation of successive profitable degrees of sterility" (8, p.361). As he subsequently noted "it could clearly have been of no advantage to such separated species to have been rendered mutually sterile, and consequently this could not have been effected through natural selection" (8, p.379). In other words whatever genetic factors had maintained reproductive isolation would have had to have been found purely through chance alone- a blind walk through genetic space in search of those mutations that would prevent reproduction between some individuals and allow reproduction between others (9).
Rather than supporting evolutionist dogma the picture of coordinated changes being effected in individuals numerous enough so as to ensure the creation of novel species resonates more closely with the tenets of intelligent design. It is the height of irony that evidence-lacking meanderings over evolution and speciation should become most apparent in the 'gut feelings' of the humble fruit fly.
1. Jeff Akst (2010) Gut Bugs Affect Mating, The Scientist, 15th December, See http://www.the-scientist.com/news/display/57793/
2. Gil Sharon, Daniel Segal, John M. Ringo, Abraham Hefetz, Ilana Zilber-Rosenberg, Eugene Rosenberg (2010) Commensal bacteria play a role in mating preference of Drosophila melanogaster, Proc Natl Acad. Sci USA Vol 107, pp. 20051-6
3. Stephen Jay Gould (2002) The Structure of Evolutionary Theory The Belknap Press of Harvard University, Press Cambridge, Massachusetts, pp.800-802
4. Niles Eldredge (1985) Time Frames: The Rethinking of Darwinian, Evolution and the Theory of Puctuated Equilibria, Published by Simon and Schuster, New York
5. Laura Reed, Therese Markow (2004) Early events in speciation: Polymorphism for hybrid male sterility in Drosophila, Proc Natl Acad. Sci USA Vol 101 pp. 9009-9012
6. A Gene Responsible for Hybrid Incompatibility in Drosophila, PLoS Biology Vol. 2, Issue 6, p. 709
7. Daniel A. Barbash, Philip Awadalla, Aaron M. Tarone (2004), Functional Divergence Caused by Ancient Positive Selection of a Drosophila Hybrid Incompatibility Locus, PLoS Biol. 2004 Jun;2(6):e142.
8. Charles Darwin (1859) The Origin of Species By Means of Natural Selection Or The Preservation of Favored Races In the Struggle For Survival Modern Library Paperbacks Edition (1998), New York
9. Darwin stipulated that in order for speciation to have segregated populations into reproductive isolates, so-called "disturbances" in the genetic makeup of offspring must have occurred whenever there were crossings between species. But natural selection could not have been the mechanism that led to hybrid incompatibility. Since natural selection favors those traits that are advantageous to an individual within a population, what advantage could be gained from one individual becoming reproductively isolated from the rest of its neighbors? Without the ability to reproduce no genes would be carried over to successive generations. Several individuals would have had to evolve their speciation genes in precisely the same way as to give a genetic constitution that was sexually compatible, this through chance alone.
Unlike Darwin's bicentennial, here is one anniversary that is certainly worth celebrating. Unlike Darwin's rock pile, here is one example of how the science of today is building on the solidity of yesteryear's durable substructure. Anti-evolutionists are not anti-science. But they are opposed to the beligerence of those who contumaciously refuse to accept the broader implications of science's beautiful procession towards the truth.
Written by Felipe Aizpun Vines, OIACDI; 2010, ISBN 10-1452800790; Review by Carlos Javier Alonso, University of Navarra, Spain (see original review in Spanish at OIACDI); Translation by Robert Deyes
Evolucionismo y conocimiento racional (Evolution and rational thought) presents a thoroughly comprehensive analysis of both the arguments in favor and against evolution and demonstrates the author's deep understanding of scientific literature published over the last few decades on the subjects of life's origins and the evolution of man. This timely volume deals with the subject matter in extraordinary depth through its coverage of both classical and contemporary viewpoints from the various schools of evolutionary thought. The 622-page text of Evolucionismo y conocimiento racional is divided up into 21 chapters that systematically unpack the following topics: Darwinism, Evolution: fact or theory, materialist prejudices, creationism, fundamentalism, rational thought, science and philosophy, routes of reason, shortcomings of the scientific method, the 'new biology', intelligent design, evolution and creation and the philosophy of life.
Evolucionismo y conocimiento racional stands out as a resource that brings together the core elements of the topics it covers and thus provides an avenue for readers to assess the current state of debate. In this regard Evolucionismo y conocimiento racional can be seen as the 'evolution bible'. Rather than giving the impression of a rapidly assembled collection of facts put together for the sole purpose of disseminating information, the book bears all the hallmarks of a well thought out literary masterpiece. Most notable is the rich collection of arguments through which each of the evolutionary hypotheses are expounded and systematically considered. And yet Evolucionismo y conocimiento racional is not exclusively directed towards specialist readers. On the contrary. In my assessment, it is easily accessible to those who have a basic training in philosophy and science and a firm grasp of the multi-faceted problems surrounding evolutionary reasoning.
Understood in a purely biological context, evolution is not a fact in itself but rather an interpretation of the facts as we find them. To be sure, no scientific specialty can claim to faithfully reconstruct what happened hundreds of thousands let alone millions of years ago. The relevant disciplines only allow us to make conjectures or presumptions regarding the journey that evolution has taken. It therefore follows that evolution carries with it an inherent (not necessarily false) bias and constitutes a hypothesis lacking the empirical support so necessary to establish it as a scientific theory.
Criticisms of the Darwinist paradigm and its neo-Darwinist reformulation are sufficiently convincing, not easily refutable and solidly rigorous. As Felipe Aizpun shows, Darwin's lack of understanding of genetics prevented him from drawing up a mechanism through which evolution could run its course. But the neo-Darwinist revision fares no better. The proposed combination of favorable random mutations preserved by natural selection falls short in every aspect.
The author compellingly asserts that the chance assessment of events exists nowhere other that in the minds eye. There are numerous causal factors that can affect the outcomes of natural processes and there is no way to predict which factors will act to produce a given outcome. The complexity of nature makes such predictions very difficult if not impossible given that causal factors that act in one instance might be absent in others. An appeal to 'chance' is an appeal made from ignorance of what causal factors are at play in the manifestation of a reality that we observe. Only in relation to a partial cause can we talk about chance. For these reasons the Darwinian paradigm, defined in Kuhnian terms, is one that is rife with anomalies and thereby one that is on the verge of a revolutionary crisis. While the alternative offered by Professor Maximo Sandin and biologist Lynn Margulis amongst others still carries with it significant gaps in understanding and points of contention (these are discussed with noteworthy precision and clarity in chapters 17 and 18) it could still unseat the official paradigm in the short term not only because of its more coherent consideration of the facts but also because the causal factors it invokes better explain the phenomenon of evolution.
Evolucionismo y conocimiento racional supplies an accurate analysis of scientific naturalism which at its core reduces all understanding to that which is experimentally demonstrable. Scientific naturalism is a theory that states that only experimental science can provide a valid understanding of reality and that scientific investigation alone meets the needs of human intelligence. In accordance with this doctrine there has been a pinning down that unjustifiably restricts all human understanding to the confines of science. Nevertheless we cannot lose sight of the fact that science is not the only system available to us for acquiring knowledge. Undoubtedly a large part of what we know and what we have achieved has come to us from sources outside the scientific enterprise. The avenues along which man can understand reality are many. Beyond genetic inheritance, traditions and personal experience as well as art, crafts, religion, poetry and philosophy can provide a basis for understanding diverse aspects of our experience. While scientism claims that knowledge of our world is limited to that which is obtainable through experimental science, reducing all objectivity to that which is experimentally acquired blinds us to the fact that the scientific/natural picture is only one branch of the total human experience.
Another matter deserves our attention- the criticism (in my opinion questionable) of Tomist metaphysics and of the evidential force of his five arguments for the existence of God. According to the author such arguments imply the possibility of demonstrating the existence of God deductively. The author displays a partiality towards inferring the existence of God in probabilistic terms in accordance with the abductive line of reasoning put forward by Charles Sanders Pierce. A consideration of God's existence through probability rather than certainty, the latter being in accordance with a deductive mode of reasoning, has important ramifications. For example, a discourse on the foundations of morality on God would only fit into the religious context of revelation and would require from us additional efforts if we were to find an exclusively rational explanation, understood as an unavoidable commitment to action that could elude the subjectivist and relativist trap to which we would be destined.
Regarding this point the author reveals himself to be a partial doubter of the Kantian epistemology and criticism of the Tomist arguments. In his view, the Kantian criticism is made up of two parts that need to be differentiated. On the one hand we are to reflect on the fact that the deductive process for a cosmological argument is inconsistent given that it assumes an identification of the ideal concept of the necessary being with the being of realism even though such a connection is not rationally admissible. On the other hand, Kant concludes equivocally, taken by an arbitrary epistemological limitation, that transcendent ideas are inaccessible to reason. Although accurate the Kantian criticism of the Tomist approach, notes the author, the idea that God is not foreign to our rational state and the Kantian conclusion of unknowability, does not necessarily follow. What needs to be defined is an adequate method of reasoning that takes us to a primary cause and its connection with sensible knowledge.
One has to specifically acknowledge that there is something that is simply erroneous in the statement that knowledge exists exclusively as a function of sensible knowledge. Such a stance implies a rejection of formal abstraction and the separation of diverse aspects of being such as the modes of cognitive access and reality. To negate such an abstraction and separation is to obstruct the pathway towards God, given that we will not be able to access the being of those creatures.
Evolucionismo y conocimiento racional falls firmly within the paradigm of Intelligent Design. Seen from our vantage point, the design inference that comes from the study of living creatures is a completely logical one (one has to be blind not to see this); this is the inference that the latest theories- both theistic and more recently those of intelligent design- have put forward both in philosophical and scientific circles; such theories have generated much animosity amongst Darwinists, with their fundamental assumption of natural selection acting on random mutations. In any case, one has to recognize that all theories categorized under the ID umbrella play on two fields: that which argues strictly on scientific grounds (the work of Behe and Dembski concerning irreducible complexity and specified complexity in addition to their critique of the neodarwinist explanation, are paradigmatic examples of this) and also that which argues on philosophical grounds since they postulate the existence of a Designer as the causal agent that is necessary for the design. Within this perspective, ID theories do not fit strictly into the experimental scientific method and can therefore be considered as non-scientific. Nevertheless this does not mean that they are false since reality is not confined to that which we can observe through experimental science. Rather it means that these theories are at the same time both scientific and philosophical in nature.
In view of these points, Evolucionismo y conocimiento racional is a must-read for those wishing to remain up-to-date with contemporary evolutionary theories and the arguments that support them.
Dr. Carlos Javier Alonso obtained his PhD in philosophy from the University of Navarra in Spain. He also holds a degree in hispanic philology from the University of Leon and is an associate professor at the Instituto de Educacion Secundaria Ordono II in Leon. He is the author of several books on science including El Evolucionismo y Otros Mitos: La Crisis del Paradigma Darwinista (transl. Evolutionism And Other Myths: The Crisis Of The Darwinist Paradigm)
By Robert Deyes
The blogosphere is brimming with commentaries over the ever-visible changes that usher in the arrival of Autumn in the northern hemisphere (1). The beckoningly bright colors of the foliage on our trees and the seasonal appearance of pumpkins that adorn our porches and abound in the fields around our cities serve as reminders of a festive transition. Throw the occasional honking of migrating Canadian geese into the mix and it is easy to see why many of us cannot help but momentarily stop in awe. The geese in particular are my gaze-catchers. Craning my neck as I look straight up I have become obsessed with capturing the flight of these birds on camera.
But there is more that interests me about Canadian geese than simply their migratory 'order of business'. Unknown to many a bird watcher, Canadian geese are one of several 'gold mine' species that harbor a strain of bacteria called Bacillus licheniformis in the tufts of their plumage (2). These feather-degrading bugs are prevalent in all manner of ground-foraging birds and occur in greatest numbers during the late autumn and winter months. Because of their tough keratin-rich microfibril composition, feathers are extraordinarily resistant to biodegradation (2). But not so tough that keratinolytic bacteria such as B. licheniformis cannot break them down (2). And biotechnologists are exploiting this ability to the full.
B. licheniformis has spawned much excitement in the agricultural world (3). Bird feathers are routinely used in animal feed. But until the early 1990s steaming was the only means by which they could be made more digestible (3). Scientific acumen and ingenuity changed all that. By putting B.licheniformis to work on a feathery meal, an inter-disciplinary group from North Carolina State University generated "appreciable degradation products" of digestible protein (3). In so doing they opened the door for a commercially-viable process that improves on the nutritional value of traditional steaming methods.
And its agricultural relevance has not stopped there. This multi-purpose bacterium is also finding application in pest control as a pre-harvest treatment for eradicating diseases that attack fruit (4). Mangos, which today constitute "one of the most important fruit crops grown in tropical and subtropical regions" have been targeted for trials against bacterial blackspot (Xanthomonas campestris), anthracnose and soft rot (4). Chemical treatments such as Copper Oxychloride have been heavily legislated against because of their detrimental effects on soils (4). B.licheniformis has proven to be an effective antagonist against these diseases and is therefore gaining traction as the way of the future for pest control.
Enzymes are commonly deployed in laundry products where they function as potent digesters of dried-on grime. And those of B.licheniformis are best-in-class when it comes to getting the job done. Look down the ingredients list of most brands of washing powder and you are likely to find two components- alpha-amylase and Subtilisin-A- that respectively perform the job of breaking down starch and proteins (5). Thankfully detergents do not adversely affect the ability of these enzymes to get to work on food splurges (6). Microbially-derived proteases form more than half of the industrial enzyme market (6). And those of alkaline-dwelling organisms such as B.licheniformis are particularly attractive given the high pH of laundry detergents (9.0-12.0) (6).
B.licheniformis has also joined a fast growing club of microorganisms able to synthesize gold nanoparticles which are used in the development of pharmaceuticals (7). Microorganisms such as B.licheniformis carry periplasmic proteins on their outer surface that bind and reduce Aureum Chloride and in the process generate 10-100nm sized nanoparticles that can be isolated from the bacterial fraction as a dried powder (7). The microorganismic approach to gold nanoparticle production has the unique advantage of being more ecologically sound than current procedures that use harmful reducing agents (7).
From our houses to our farms and onwards into the pharmaceutical development lab B.licheniformis is fast becoming an indispensable workhorse. Its many secrets are being exploited in novel ways. And its revolutionary attributes continue to amaze. Higher eukaryotes sport elaborate olfaction mechanisms to detect gas molecules (8). Up until earlier this year there had been no reports of similar mechanisms in bacteria (8). All that changed with the news that a couple of European biotechnologists had incontrovertibly demonstrated olfaction in B.licheniformis cultures (8). By putting B.licheniformis adjacent to inducer strains of B.subtilis, M.luteus and E.coli, Reindert Nijland and J. Grant Burgess observed notable color changes and a tendency for formation of dense pellicles (known in the trade as biofilms) (8,9). Some simple experiments gave Niijland and Burgess the clues they needed to home in on the molecular exchange that lay at the heart of this response- a rise in concentrations of gaseous ammonia (8,9).
Seen in the wider context of the discoverability of our planet that authors such as Guillermo Gonzalez, Jay Richards and Michael Denton have exposed in their best-selling tomes, B.licheniformis is just one of a vast number of available resources that are helping us reshape the way we live. "The stupendous success of science since 1600" writes Denton "is testimony enough to the remarkable fitness of our mind to comprehend the world" (10). "We've seen that scientific progress and discovery depend on nature being more than meaningless matter in motion...It's an exquisite structure that preserves vast stores of information...We in turn possess the materials and the physical and intellectual capacity to create technologies...As eyeglasses and light bulbs have improved our ability to read written texts so the microscope and telescope have allowed us to read the book of nature more deeply...The myriad conditions that make a region habitable are also the ones that make the best overall places for discovering the universe in its smallest and largest expressions" (11).
Whether the olfaction aptitude of B.licheniformis can be translated into a useful application that aids in the "betterment of human life" (in accordance with the biotechnologists' mantra, 12) remains to be seen. Yet the story of this robust microorganism seems far from over. And as the geese continue to pass overhead during this yearÃƒÂ¢Ã¢â€šÂ¬Ã¢â€žÂ¢s autumnal leaf-fall I cannot help but see it as a bacterial 'high-flyer' that has taken center stage in the biotechnology arena.
1. Sara Klink (2010) A Time For Harvest, Promega Connections, September, 24th, 2010, See http://promega.wordpress.com/2010/09/24/a-time-for-harvest/
2. Edward Burtt, Jann Ichida (1999) Occurrence of feather-degrading bacilli in the plumage of birds, The Auk, See http://findarticles.com/p/articles/mi_qa3793/is_199904/ai_n8834646/
3. C.M.Williams , C.S Richter, J.M. MacKenzie Jr, Jason C.H. Shih (1990) Isolation, Identification and Characterization of a Feather-Degrading Bacterium, Applied And Environmental Microbiology, Volume 56 (6), pp. 1509-1515
4. Evaluation of pre-harvest Bacillus licheniformis sprays to control mango fruit diseases, Crop Protection, Volume 26, pp. 1474-1481
5. Measurement of endo-Protease and ÃƒÅ½Ã‚Â±-Amylase in Biological Washing Powders & Liquids using AZO CASEIN and AMYLAZYME TABLETS www.megazyme.com/GetAttachment.aspx?id=17e0f84c-9ba1
6. Nedra El Hadj-Ali, Rym Agrebi, Basma Ghorbel-Frikha, Alya Sellami-Kamoun, Safia Kanoun and Moncef Nasri (2007) Biochemical and molecular characterization of a detergent stable alkaline serine-protease from a newly isolated Bacillus licheniformis NH1, Enzyme and Microbial Technology, Volume 40, pp. 515-523
7. Kalimuthu Kalishwaralal, Venkataraman Deepak, Sureshbabu Ram Kumar Pandian, Sangiliyandi Gurunathan (2009) Biological Synthesis Of Gold Nanocubes From Bacillus Licheniformis, Bioresource Technology, Volume 100, pp. 5356-5358
8. Reindert Nijland and J. Grant Burgess (2010) Bacterial Olfaction, Biotechnology Journal, DOI 10.1002/biot.201000174
9. Janelle Weaver (2010) Bacteria sniff out their food, Nature 16 August 2010, See http://www.nature.com/news/2010/100816/full/news.2010.411.html
10. Michael Denton (1998) Nature's Destiny: How The Laws of Biology, Reveal Purpose in the Universe, 1st Edition Published by the Free Press, New York, p.260
11. Guillermo Gonzalez and Jay Richards (2004) The Privileged Planet, How Our Place In The Cosmos Is Designed For Discovery, Regnery Publishing Inc, Washington D.C, New York, p.334
12. Abdelali Haoudi (2003) New Forum for Innovative Research in Biomedicine and Biotechnology, J Biomed Biotechnol. 2003, Issue 3, p.161
During the 1990s I had untold opportunities to witness the full exuberance of nature's rich offerings. My parents' house on the southwestern edge of Ecuador's capital Quito was set in a prime location for observing all manner of wildlife. And most memorable of all were the hummingbirds that frequented our garden attracted as they were to the blooming plants that had been strategically potted next to the outside walls of our living room. These veritable masters of flight, the smallest of warm blooded creatures on our planet, arrived with the sole purpose of extracting sweet nectar from the flowers we had laid before them. Their hovering maneuverability was their most striking attribute.
To date over 330 different species of hummingbird have been identified across the expanse of the American continent (1-3). And the mechanisms behind their supreme agility are being dissected out by the likes of UC Riverside biologist Doug Altshuler (1,4). Using revolving feeders filled with nectar and cameras that record minute positional adjustments relative to feeder rotation, Altshuler has uncovered one of the secrets behind these birds' exquisite capabilities: flexible rotating shoulder bones that allow them to hover while maintaining their bills firmly inside flowers (1,2). With little to no opportunity to perch during feeding, their wing anatomy is indispensable for survival (1). On average 'hummers' consume more than half their body weight in nectar extracted from as many as 1000 flowers each day (1). To sustain this extraordinary rate of consumption their berry-sized hearts must beat 600 times a minute during rest and almost double that during flight (1). This totals up to 4.5 billion times during their 12-17 year lifespan (4). A continuous feeding binge supplies them with the energy they need to beat their tiny wings a staggering 80-200 times per second (1,2).
In the mountain forests of Ecuador, not far from where my parents lived, there exists a species of hummer whose popular name, the swordbill, accurately describes the appearance of its feeding accoutrement (1,5). With its four inch beak the swordbill is able to feed on the nectar of the Datura plant (1,5). And it turns out that it is uniquely equipped for the job. Because Datura blossoms hang straight down, a four inch bill is what it takes to gorge on the effusions coming out of nectaries at the very base of the flower. But there is a trade-off. As the bird feeds, it is dusted with pollen that it carries to its next port of call (1).
Although hummers are built to feed on nectar, they cannot sustain themselves on sugar alone. They depend heavily on insects as a primary source of protein (3). It is little wonder then that bugs form 1/4 of their daily diets (1). With deadly accuracy hummers can pick out their prey mid-flight by opening their flexible bills to the widest capture position possible (1). And that is not the only way their bills are so refined for the functions they perform. Today eight thousand plant species depend on the hummer for pollination. Like a lock and key, each bill fits into a limited set of blossoms. The Purple-throated Carib even exhibits marked gender differences in bill length tailored as they are to feed on different species of the colorful Heliconia plant (1).
At nighttime hummers thwart the clutches of starvation by fluffing up their feathers to conserve heat and entering into a low energy sleep state called Torpor (3). By lowering their heart rates to a sluggish 36 beats per minute and their body temperatures from a comfortable 105 degrees Fahrenheit to the 'hypothermic threshold' of life, they barely manage to stay alive (1,3). The process is easily reversed however. And when day breaks, vital signs ramp up to normal in 20 minutes or less in readiness for another day of high cost flying (3).
Flight behaviors amongst hummers challenge even our most optimistic preconceptions of avian aerobatics. UC-Berkeley biologist-engineer Chris Clark has captured the steep death-defying 60 miles/h dive of the male Anna's on camera as they perform a carefully choreographed mating display (6). By taking high definition shots at 500 frames per second Clark estimates that g forces in the Anna's dive match those at which military fighter pilots black out (1). Males descend at such an angle and speed that their tail feathers vibrate at the appropriate acoustic frequency to woo female onlookers (6). When it comes to heroic feats, most hummer votaries will wax lyrical over the seasonal migrations of their feathered icons. Licensed 'banders' devote much time to the study of feeding and migration habits by crimping tiny uniquely-coded metal rings onto the hummers' toothpick-sized legs (7,8). And their work has brought the hummers' continent-wide peregrinations into sharp focus. Some fly as many as 6000 miles between North and Central America breeding in the temperate zones of the north and wintering in the warmer climes of the south (3). One species, the Ruby Throat, even endures an 18 hour, 500 mile long trek across the open waters of the Gulf of Mexico with no place to stop or feed, by storing the extra 2-3 grams of fat it needs to make it across (3).
The hummer story tells of irreducible complexity at key levels of functionality. Anatomically these birds require not only a unique hovering system and long beaks but also a heart that can keep up with their voracious appetites. And the exacting nature of their specific behaviors leaves little room for evolution's undirected mutational 'potshots'. Species like the Ruby Throat, for example, need to binge on the grub that will get them through their sea-crossing expedition. But their food quota must be carefully regulated. Too little nourishment means not enough energy to make it across. Too much nourishment and they risk over-weighting themselves and plunging into the unrelenting waters below.
There is one hummer that is indelibly etched into my wish list of nature's must-sees- the Peruvian Spatuletail (9). The furious waving of its long tail feathers during courtship has recently been captured on camera (9). And like everything else in the hummer, these movements are made at neck-breaking speed (9). The Spatuletail waves the spoon-shaped spatules at the ends of its feathers while hopping on a twig 14 times a second (10). Awakened by such feats, my parents and I indulged in a little ecotourism by traveling down to the Maquipucunia nature reserve about 50 miles to the north of Quito in Ecuador (9). Even though we knew little about the birds that graced the hills of this unspoiled paradise, we were able to appreciate the numerous hummers as they flaunted their iridescent colors. The setting could not have been more visually arresting. And while we never made it down to Peru what we saw more than made up for that particular missed opportunity.
1. Hummingbirds: Magic In The Air, See PBS Nature Special at http://www.pbs.org/wnet/nature/episodes/hummingbirds-magic-in-the-air/introduction/5424/
2. Mike Klesius (2007) Hummingbirds: Flight Of Fancy, National Geographic, January 2007, See http://ngm.nationalgeographic.com/2007/01/hummingbirds/klesius-text/1
3. How do Hummingbirds survive cold nights? Hummingbirds and Torpor, See http://scienceblogs.com/grrlscientist/2006/04/hummingbirds_and_torpor.php
4. Biologist's Lab at UC Riverside Is a Hummingbird Health Spa, See http://newsroom.ucr.edu/news_item.html?action=page&id=2233
5. Mary O'Leary (2009) Local filmmaker captures hummingbirds for PBS, New Haven Register, December 27th, 2009, See http://www.nhregister.com/articles/2009/12/27/news/new_haven/doc4b36ce70697f1930415349.txt
6. Robert Sanders (2008) Anna's hummingbird chirps with its tail, http://berkeley.edu/news/media/releases/2008/01/30_hummingbird.shtml
7. Like Banding A Toothpick! Talking With Sarah Driver, Hummingbird Bander, See http://www.learner.org/jnorth/tm/humm/HumBander_Sarah.html
8. Hummer/Bird Banding Research Collaborative (HBBRC) http://www.hbrcnet.org/index.htm
9. The Maquipucunia Reserve: http://maqui.myweb.uga.edu/
10. Matt Walker (2009) A Marvelous Hummingbird Display, BBC Earth News, 3rd November, 2009, http://news.bbc.co.uk/earth/hi/earth_news/newsid_8338000/8338728.stm
Review Of Programming of Life By Donald Johnson, ISBN-10: 0982355467
By Robert Deyes
There are some science writers that quite simply have a knack for combining the detail of their subject of expertise with a talent for exposition that a wide audience can easily understand. Donald Johnson is one of them. After carefully defining the various types of information- functional, prescriptive and Shannon- that information theorists have set out in their realm of study, Johnson takes the reader on a tour of cellular gene expression by focusing on the digital code of DNA. Shannon information, which provides a mathematical measure of improbability without regard to functionality does not help us in the description of life since the digital code of DNA is rich in what Johnson terms 'functional prescriptive information'.
While initiatives such as the Origin Of Life Prize have encouraged researchers to find non-super-naturalistic processes that might explain the origins of prescriptive information, no offerings to-date have withstood the test of scientific scrutiny. Indeed all known cases of such information invariably point to the work of a mind. Johnson emphasizes the relevance of probability in his espousal of this inference- the simplest form of life was found to be 10exp80,000 times more likely of having a mindful than a non-mindful source.
Johnson repeatedly stresses how the information content of DNA is analogous to the information carried on a computer disk drive.Within such a schema, each of the enzymes that decode the information can be seen as individual computers that bring meaning to the code through the RNA that is transcribed and the proteins that are translated. 23,000 genes make up the human genome. And the multi-functional nature of these genes in self evident in the way that RNAs are differentially spliced and glued together.
Johnson's perspective packs a might punch on the evolutionary edifice. Computer simulations and evolutionary algorithms such as MeThinksItIsLikeAWeasel and AVIDA have failed to show how evolution can generate prescriptive information since pre-specified targets, unrealistic protection of replication instructions and unrealistic energy rewards abound in each of these systems.
While the battle over the categorization of junk DNA rages on amongst biologists, Johnson gives us a succinct and well-buttressed view on the subject: "Researchers are discovering that what has been dismissed as evolution's relics are actually vital for life". There is no evidence that new prescriptive information can be built up by genetic rearrangements such as transposition, inversion, duplication or point mutation. We can therefore understand Lynn Margulis' reference to the Darwinian claim as a `half truth' grounded in religious ferocity. This half truth forms the foundation for Johnson's final attack as he considers the merits of irreducible complexity and Craig Venter's recently produced artificial genome. Rather than showing how an organism could arise from scratch, Venter's enterprising achievement revealed the need for careful engineering of existing parts into a form that could be introduced into an existing organism.
Johnson's writing style is captivating. The extensive range of resources he draws from only serves to build confidence in the factual accuracy of his case. What a terrific read. Sheer brilliance.
By Robert Deyes
When I first picked up neurobiologist Jerome Siegel's recent Nature review on the evolutionary significance of sleep, I was expecting to find a scientifically-buttressed counter-position to the age-old assertion that describes sleep as "a vulnerable state...incompatible with behaviors that nourish and propagate species". Siegel's evolutionary discussion was nonetheless unconvincing (1). While he supplied a nice primer on the neurobiology of sleep, Siegel gave no real riposte to the outstanding question of survivability posed above other than to iterate a rather uninformative statement: "In each species the major determinant of sleep duration is the trade-off between the evolutionary benefits of being active and awake and those of adaptive inactivity" (1).
To understand why Siegel fell short it is important to re-familiarize ourselves with the rich diversity of sleep behaviors that we find in the mammalian world. Children learn about these behaviors from an early age: giraffes nap for anywhere between 10 minutes to two hours, elephants for five hours and anteaters for as long as fourteen hours (2). Marine mammals exhibit their own unique sleep patterns, notably a unilateral (unihemispheric) slow down of brain wave activity (contrast this with the bilateral (bihemispheric) slow down of non-REM sleep in land mammals) (1,3). And seals make use of both bilateral and unilateral modes depending on whether they are in terrestrial or aquatic environments (1,3). Researchers readily proclaim that "mammalian sleep is extremely diverse" with the unihemispheric sleep of dolphins being "nothing like the rapidly cycling sleep of rodents, or the single daily block of humans" (3).
While a direct correlation between body mass and sleep quantity has been reported in herbivores, the impact of mass and other physiological variables on sleep patterns across the animal kingdom remains highly controversial (1). Moreover there appear to be significant mammalian species-specific differences regarding the lethality of sleep deprivation as well as in hormone release patterns during sleep and wake times (1). In all three subclasses of mammals (placentals, marsupials and monotremes) there are noticeable differences in REM/NON-REM sleep patterns. Extant monotremes for example are unique in their display of brainstem associated REM and forebrain Non-REM (1).
Many mammals and several invertebrate species can regain lost sleep (sleep rebound) in about 30% less time than it would have taken during their normal sleep routine (1). Understandably evolutionists have pondered over the question of why in such cases shorter sleep durations and concomitantly longer wake times have not evolved so as to maximally capitalize on opportunities for hunting and foraging (1). Strikingly dolphins, killer whales and seals can survive the winter months without sleep rebound after extended periods of activity in the open sea (1). In all, these results are at odds with the expectation that sleep would be "physiologically similar across mammals" (1).
Speculation over why animals would spend significant portions of their lives in vulnerable states of dormancy has focused on the benefits of brain energy conservation and the concomitant reduced risks of injury and detection by predators. Siegel defined the adaptive benefits of sleep as the suppression of activity at times that have "maximal predator risk and minimal opportunity for efficiently meeting vital needs" and the allowance of activity at times of "maximal food and prey availability and minimal predator risk" (1). Yet in light of the rather complex and varied sleep behavior patterns described thus far, Siegel's conclusions seem empirically un-testable. How can we truly ascertain whether some poorly defined threshold of ill-timed predatory risks and inefficient brain energy conservation has been reached?
If anything real life observations contravene expectations. A few examples make this plainly clear: the 19th century zoologist James Edward Gray recorded crossing paths with bowhead whales "sleeping so soundly a few meters from the pack ice that they did not even react to his approaching boat" (4). Owls are prone to large mob lynchings from hawks, crows and jays as they doze atop exposed tree trunks (5). Humming birds make themselves susceptible to attack by adopting an almost lifeless state called torpor as part of an energy-recovery sleep regimen (3). And mortality in certain reef teleost fish is higher during the night when resting than during the day when swimming in open waters (6). Such life-threatening vulnerabilities do not support the existence of trade-offs acting as effective evolutionary operatives over the course of time as Siegel might have envisaged.
World-renowned biochemist James Krueger concurs- sleep is by all counts maladaptive unless "a greater need is served" (7). What that need might be remains to be seen although there is no shortage of ideas. Krueger for example believes that sleep may somehow facilitate the integration of new memories into existing neuronal circuits (7). Some speculate that sleep serves the role of removing dangerous free radicals from the brain . Others hold to the veracity of the Null Hypothesis which, simply stated, maintains that sleep is nothing more than "a kind of extreme indolence that animals indulge in when they have no more pressing needs, such as eating or reproducing" . Sleep quite clearly performs a restorative function although the exact details have eluded even the most dedicated of investigative minds . In what way can the current data be reconciled with a picture that shows sleep behaviors evolving as a result of selective pressures across the millennia?
In the June, 2010 issue of PLOS Computational Biology, a cross-disciplinary group from the University of Sydney and Harvard Medical School headed by Amesh Abeysuriya provided what was touted as the definitive answer to this question (3). At the heart of mammalian sleep behaviors is a collection of diverse molecules called somnogens that accumulate during wake times and generate a "homeostatic drive to sleep". Cells in the monoaminergic brainstem nuclei (MA) and the ventro lateral preoptic area of the hypothalamus (VLPA) form what Abeysuriya et al consider to be a sleep-wake switch that functions through antagonistic inhibition (3). For aquatic mammals in which unihemispheric activity is observed, a "mutually inhibitory connection" is thought to exist between VLPA populations that prevents both hemispheres being activated simultaneously. Abeysuriya et al devised a model that they claim accounts for the sleep patterns observed in 17 species of mammals (3).
Krueger is one of a handful of sleep experts who believe that sleep is not an "all or nothing" affair even in bihemispheric-operating mammals (9). Krueger has proposed that in all mammals groups of neurons can be selectively shut down after being used for the tasks they routinely perform (4). What we call sleep might therefore simply be a state in which a large number of neurons have been shut down to the extent that they are no longer able to function (9). Washington State University electrophysiologist David Rector has built up enough hard evidence to support such a proposal. Following experiments with lab rats Rector is confident that "there's no central control, no on-off switch". He remains adamant that the need for sleep arises as a result of the progressive use of neuronal cell clusters over the course of a wake period (9).
Several somnogens have now been extensively reported on in the peer-reviewed literature (3). The universality of the homeostatic drive that results from these somnogens coupled with the MA-VLPA cellular interactions have led Abeysuriya et al to conclude that differences in sleep patterns across species represent nothing more than evolutionary attenuations of a system that existed before mammals roamed the earth (3). But blatantly lacking in this evolutionary picture is a genetic basis for explaining how these attenuations supposedly came into effect. Ever since the early 1970s, when researchers began a frantic search for a mysterious sleep hormone dubbed "Factor S", the idea of a single sleep gene has been gradually but emphatically turned on its head (7,9). There are now over a hundred such genes, most of them encoding a class of immune proteins called cytokines, that in one way or another play a role in regulating sleep patterns (7,9). Of these there are about fifteen big players with TNF, IL-1, Growth Hormone Releasing Hormone (GHRH) and adenosine (with its receptor) being perhaps the best characterized of them all (3,9,10).
A complex network of positive and negative feedback loops called the sleep homeostat forms the molecular foundation of non-REM phase sleep which varies predictably in response to physiological cues such as feeding and illness (10). Importantly Krueger's research has brought into sharp clarity the role of a gene called preproghrelin which is now known to modulate sleep and regulate body temperature as a function of food availability (11). The preproghrelin gene expresses multiple protein products one of which, the ghrelin hormone, acts in suppressing sleep during bouts of hunger (11). Another preproghrelin product, the obestatin hormone, induces sleep and maintains stable body temperatures when food is scarce (11). These antagonistic functions are critical for survival in the wild where "natural shortages of food and low environmental temperature are commonly encountered" (12). Indeed preproghrelin gene knockout mice have been shown to suffer from severely disrupted sleep and uncontrollable hypothermia when doubly challenged by an absence of food and cold external temperatures (12)
Any model that purports to explain the evolution of sleep throughout nature has to account for the multi-layered genetic and cellular complexity that undergirds its panoply of forms. Clearly involved are exquisitely regulated and species-tailored communication systems, with key biological processes and molecular determinants playing an integral role in sleep/wake regulation. None of the work to-date on evolution has given us much beyond deeply-held assumptions served up in a manner that leaves out the full extent of what we now truly know about this captivating topic. It can be said that at its core the current evolutionary story has become nothing more than the materialists' dreamy solution to a nightmare of a problem.
1. Jerome M. Siegel (2010) Sleep Viewed As A State Of Adaptive Inactivity, Nature Rev Neurosci, Volume 10, pp. 747-753
2. Richard and Louise Spilsbury, A Herd Of Elephants, Heinemann Library, p.20; Jennifer McDougall, Giraffes, Scholastic, p.25; Lorien Kite, Anteaters, Grolier Educational, p.30
3. Andrew J. K. Phillips, Peter A. Robinson, David J. Kedziora , Romesh G. Abeysuriya (2010) Mammalian Sleep Dynamics: How Diverse Features Arise from a Common Physiological Framework, PLOS Computational Biology, June 2010, Volume 6, Issue 6, e1000826
4. Jacques Cousteau and Yves Paccalet (1986) Whales, W.H. Allen & Co, London, pp. 219
5. Helen Rodney Sattler (1995) The Book Of North American Owls, Clarion Books, NY, p. 23
6. Chiara Cirelli, Giulio Tononi (2008) Is Sleep Essential? PLOS Biology, Volume 6, Issue 8, e216
7. Tim Steury (2010) Why Do We Sleep?, Washington State Magazine, See
8. The New Book Of Popular Science, Volume 5, Grolier Publishing, pp. 405-409
9. Cherie Winner (2006) The Secrets Of Sweet Oblivion, Washington State Magazine, See http://wsm.wsu.edu/s/index.php?id=130
10. James M Krueger, David M Rector, Sandip Roy, Hans P A Van Dongen, Gregory
Belenky, and Jaak Panksepp (2008) Sleep As A Fundamental Property Of Neuronal Assemblies, Nat Rev Neurosci Volume 9, pp. 910-919
11. Eat, sleep, stay warm: How our bodies find the right balance, See
12. Eva Szentirmaia, Levente Kapa, Yuxiang Sun, Roy G. Smith, and James M. Krueger (2009) The preproghrelin gene is required for the normal integration of thermoregulation and sleep in mice, PNAS, Vol. 106, pp.14069-14074
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Evolution has become a favorite topic of the news media recently, but for some reason, they never seem to get the story straight. The staff at Discovery Institute's Center for Science and Culture started this Blog to set the record straight and make sure you knew "the rest of the story".
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We are a group of individuals, coming from diverse backgrounds and not speaking for any organization, who have found common ground around teleological concepts, including intelligent design. We think these concepts have real potential to generate insights about our reality that are being drowned out by political advocacy from both sides. We hope this blog will provide a small voice that helps rectify this situation.
Website dedicated to comparing scenes from the "Inherit the Wind" movie with factual information from actual Scopes Trial. View 37 clips from the movie and decide for yourself if this movie is more fact or fiction.
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Most guys going through midlife crisis buy a convertible. Austrialian Stephen E. Jones went back to college to get a biology degree and is now a proponent of ID and common ancestry.
Complete zipped downloadable pdf copy of David Stove's devastating, and yet hard-to-find, critique of neo-Darwinism entitled "Darwinian Fairytales"
Intelligent Design The Future is a multiple contributor weblog whose participants include the nation's leading design scientists and theorists: biochemist Michael Behe, mathematician William Dembski, astronomer Guillermo Gonzalez, philosophers of science Stephen Meyer, and Jay Richards, philosopher of biology Paul Nelson, molecular biologist Jonathan Wells, and science writer Jonathan Witt. Posts will focus primarily on the intellectual issues at stake in the debate over intelligent design, rather than its implications for education or public policy.
A Philosopher's Journey: Political and cultural reflections of John Mark N. Reynolds. Dr. Reynolds is Director of the Torrey Honors Institute at