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The 2005 International Conference on Natural Computation will feature the most up-to-date research results in computational algorithms inspired from nature, including biological, ecological, and physical systems...[more]

An enormous team of Chinese researchers have produced an improved map of the rice genome, and have proposed that new species and new functions in rice arose evolutionarily on the basis of a mutation-duplication mechanism whereby the genome ‘tests’ mutations for efficacy...[more]

A team of cognitive researchers investigating the bottlenecks in mental response to complex tasks proposes a stochastic model of cumulative evidence for modeling response times and processing ...[more]

IEEE Conference on Computational Complexity: June 12th - 15th, 2005, San Jose, California... [more]

An international group of researchers, including members of the Santa Fe Institute and the University of Austin in Texas, has applied methods of contact network epidemiology to demonstrate that the outcomes of SARS disease outbreaks may have very different outcomes with minimal differences in initial infection patterns and outbreak conditions. They offer quantitative insight into the heterogeneity of SARS outbreaks worldwide...[more]

In an attempt to converge results for computational genomic analysis on Darwinian macro-evolutionary assumptions, a computational biologist has invented a putative standard for genomic analysis which effectively maximises the likelihood of finding conserved sequences based on chosen constraints and, and in so doing rejects methods with more rigorous constraints that result in lesser correlations. In what reads like a case study in probabilistic informational displacement and NFL, readers may find it an interesting exercise to mentally substitute the term 'complex specified sequences' for 'conserved sequences' where it occurs, and to note the reference to 'detection of a specified feature'. This research highlights the continuing acute misconception among leading scientists that chance mechanisms are adequate to explain complex specified information...[more]

Using mathematical modeling of real time data recorded via electrophysiology, researchers have employed computational methods to probabalistically extrapolate/estimate steps in signal processing within the auditory receptor cells of the grasshopper based on their output, concluding that the results could be applied to other similar mechanical-to-neural signal transduction and processing mechanisms. The sub-millisecond temporal resolution of signal processing stages is too fine, and the auditory system to delicate, to determine the bioelectrical processes by direct biophysical experimental observation...[more]

The National Science Foundation is embarking on a multidisciplinary initiative to pursue Darwin's vision of a phylogenetic Tree of Life, by conducting targeted research to resolve phylogenetic relationships for groups of organisms within the 1.7 million currently described species using new data from genetics and genome sequences, and incorporating old standards such as morphology. The NSF is placing a lot of faith in the predicted outcome, making available an estimated $29M in research grants of up to $3M to be awarded to research proposals based on eligibility as determined by the NSF and external reviewers ...[more]

Cellular development in morphogenesis of different organisms and organs usually involves complex cascades or exchanges of proteins providing signals as regulators and cues for critical phases of development such as cell adhesion. By altering levels of possible activator proteins, Elain Fuchs et al. have manipulated the expression of Snail, a regulatory protein involved in the development of hair follicles, yielding insights that may help them understand how the processes of epithelial development work in skin cancer...[more]

A burgeoning field of research in DNA science involves attempts to understand the self- assembly capabilities of complex biological molecules such as proteins and DNA by producing synthetic molecules that form periodic or aperiodic crystals, thereby demonstrating the propensity for such synthetic molecules to bind together in predictable ways. Recently, such experiments have been combined with prefatory computer simulations to produce more complex fractal aperiodic crystals based on synthetic molecules, and although the results are interesting, it is noteworthy that the self-assembling biological molecules being so 'modeled' are assumed to have evolved by Darwinian mechanisms - despite the probabilistic prohibitions of such a process occurring - and that little reference is made to the likelihood of complex self assembly capabilities arising by such mechanisms ...[more]

"The reductionist method of dissecting biological systems into their constituent parts has been effective in explaining the chemical basis of numerous living processes. However, many biologists now realize that this approach has reached its limit. Biological systems are extremely complex and have emergent properties that cannot be explained, or even predicted, by studying their individual parts. The reductionist approach—although successful in the early days of molecular biology— underestimates this complexity and therefore has an increasingly detrimental influence on many areas of biomedical research, including drug discovery and vaccine development." ...[more]

The deadly Listeria bacterium produces proteins that assist it to exploit the actin resources in a cell, appropriating and incorporating them into its own propulsion mechanism, the formation of which occurs automatically in an apparently undirected fashion referred to by researchers as emergent behavior. Researchers from the University of Washington have used computer simulation, based in part on experimental data, and incorporating numerous optimizations and much tuning, to model said emergent behavior and the operation of the resulting actin based Listeria propelling mechanical tail...[more]

Using DNA configured abstract Wang tiles in xgrow simulation software with the kinetic tile assembly model, researchers Paul Rothemind et. al have attempted to begin to gain an insight into the principles behind the rules for biochemical self assembly by generating Sierpinski Triangles with DNA binding rules computationally, and producing amazing rezults in-vitro with fractal crystal grow guided by the simulated tile configurations. This fascinating work incorporates some astonishing observations and conclusions (with actual Sierpinski Triangle fractal patterns produced in crystals in- vitro) but may demonstrate some of the hallmark problems with using in-silica simulations to draw conclusions about biochemical/biological systems, in that CSI is assumed to be the product of chance based evolution, and the methodology and experimental-simulative procedures involve the induction and imposition of externally imputed rules and parameters for cellular automata in order to obtain desired results, which are then reflected in-vitro...[more]

Introns, or intervening sequences, are significant architectural element of genes in many organisms, but why they are far less prevalent in genes of some organisms than others is not well understood. Using probabilistic analysis incorporating evolutionary assumptions - including that of evolutionary parsimony for gain and loss of introns and that common intron position in the gene indicates common evolutionary ancestry - researchers attempt to explain assumed evolutionary intron gain and loss and challenge existing wisdom that introns are biased towards the 5' end of genes in intron-poor organisms because of the effects reverse transcription...[more]

Assuming a common evolutionary genetic ancestor, researchers have attempted to explain the presence of an additional runt domain gene in the fugu pufferfish (FrRUNT) that is not present in tetrapods, which are known to possess three such genes (denoted by RUNX1, RUNX2 and RUNX3 for the human genome.) Using direct sequencing for scaffold sequences, the researchers constructed hypothetical gene structures for the fugu RD genes by maximizing similarity to known vertebrate RD proteins, and conclude that the pufferfish runt proteins must be surprisingly ancient to account for the marked divergence in the phylogenetic information of FrRUNT, and its absence in tetrapods ...[more]

To facilitate immune system response, killer T Cells rely on most nucleated cells using major histocompatibility complex proteins to present peptide (protein fragment) antigens on their surfaces, and such cells have some well known translational mechanisms for producing common AUG codon based peptides, involving tRNA and ribosomes. However, there are other 'cryptic' types of peptides produced using less well understood and novel translational mechanisms, involving CUG translation initiation codons, that researchers estimate may provide a virally stressed cell with mechanisms for avoiding the production of excess peptides based on viral protein, whilst still producing antigens for an immune system response...[more]

When exposed to oxidative stress, Escherichia coli bacterium temporarily block access to the enzyme cobalamin-independent methionine synthase (MetE) - to protect it from oxidative damage - by attaching to it a glutathione subunit. When the stress abates the MetE - which also releases Methionine as an indicator to signal stress to other bacteria in the colony - is reactivated...[more]

A study of the revertant adaption mechanism of lac- bacterial cell mutants, that are otherwise incapable of digesting lactose, in an environment where only lactose is available for consumption, is thought to demonstrate that the strict gradualist model - relying on gene amplification - for evolutionary adaption, is inadequate for explaining the mutative-adaptive response mechanism...[more]

Researchers investigating the use of Murine Leukemia Virus (MLV) and Simian Immunodeficiency Virus (SIV) as retroviral vectors for gene therapy have discovered that such retroviruses target specific gene integration sites far more often than previously assumed...[more]

New Research Institute Focuses on Complex Systems: The Internet. Human consciousness. The spread of disease such as HIV and smallpox. The U.S. power grid. Even a termite colony. These disparate systems all share one important characteristic: they are complex systems. The emerging science of complexity has attracted Northwestern faculty from a wide range of disciplines, including engineering, business and natural sciences. To take advantage of this shared interest, the University has established a new research enterprise, the Northwestern Institute on Complex Systems, whose goal is to stimulate path-breaking research of complex systems across traditional boundaries...[more]

ISCID is please to announce the latest issue of PCID, Volume 3.1 November 2004. The journal features papers from Royal Truman, Jonathan Wells, Paul Nelson and others, including several essays on the topic of irreducible complexity ...[more]

Researchers have used computational and biochemical methods to perform a structural analysis of the seven proteins comprising the yNup84/vNup107–160 subcomplex, a core building block of the eukaryotic nuclear pore complex, to investigate if it could have evolved from prokaryotic organisms with no analogous transport system. Their analysis indicates that all seven proteins contain either a â-propeller fold, an á-solenoid fold, or a distinctive arrangement of both, revealing close similarities between the nuclear pore protein structure and that of the major types of vesicle coating complexes that maintain vesicular trafficking pathways in organelles ...[more]

American and German neuroscientists have used applied statistical analysis to understand the structural and functional brain motifs, the former being related to spatial configuration and connection of nodes, and the latter defined as the combinations of information exchange on corresponding neural pathways. Their findings indicate that actual brain networks in the macaque monkey and the cat optimize for simplest structure and most complex function, which findings they seek to correlate with evolutionary hypothesis using evolutionary algorithms ...[more]

Researchers from the University of California and the Howard Hughes Medical Institute have discovered that the Ffh-FtsY GTPase protein interaction fundamental to protein targeting for various cellular processes (e.g. cytoskeletal organization, nuclear transport and spindle assembly) are surprisingly complex – more so than expected. Binding involves complex, co-ordinated interactions across the interaction surface, which requires each GTPase to contain independent interaction information that correlates in a very specific way with the information contained in the other ...[more]

New work to identify and differentiate species using DNA barcodes has provided interesting results in terms of divergence between DNA barcodes in bird populations. Researchers start with the standard assumption that the greater divergences exhibited between distant species in DNA barcodes, specifically those of mtDNA (mitochondrial DNA), are due to the faster relative evolution of mtDNA compared to other DNA types...[more]

Bioinformatics researchers have used computational techniques with a population based statistical approach that indicates that microRNA-mRNA interactions in humans exhibit markedly different behavior to the same interactions for other species such as Drosophila. According to their in-silica analysis, such coding interactions in the case of humans exhibit microRNA ‘hits’ on mRNA which extend longer than for Drosophila and sometimes with perfect complementarity, causing them to conclude that sequence complementarity, although probably the basis of how microRNA recognizes its target, has different rules for this targeting in humans...[more]

Researchers have experimental evidence that constant circadian rhythms regulate the level of the amino acid Hcy (implicated prognostically in heart disease) in blood plasma, so that peak levels occur nocturnally, possibly to help avoid cytotoxic effects in cells. Their findings indicate that the rhythms in question change according to the sleeping and eating patterns and habits of the test subjects ...[more]

With the help of Casey Luskin, Drs. Guillermo Gonzalez and Jay Richards, authors of the recently published book “The Privileged Planet”, further investigate the special conditions for life on earth, and the special advantages of observing the physical universe from earth, by focusing on the nature of earth’s paleomagnetic global fields. They demonstrate that the magnetic fields of the earth are especially conducive to life because they shield the planet’s surface from radiation and that the format, strength and distribution of these fields allow unusually accurate geological measurements, including that of the landscape of the ocean floor, and of geological history ...[more]

Astronomers analyzing image data from NASA's Spitzer infrared telescope believe that planetary formation may take up to 10 times longer than was previously believed. Findings are based on the configuration and density of planet forming disks surrounding stars of various ages ...[more]

An interdisciplinary team from Rockefeller University has extended the algorithm of Rajewsky et al., called Ahab, to incorporate two species data for probabilistic analysis. They report that their extended algorithm, named STUBB, gives improved accuracy for identification of cis-regulatory modules such as segmentation control elements when driven with cross-referenced data from the genome sequences of two species of Drosophila - D. melanogaster and D. pseudobscura ...[more]

Researchers at the Lawrence Livermore National Laboratory working with fellows from Stanford and Berkeley, have published a Web site that allows on-line identification and visualization of cis-regulatory modules in human genes. Output comes from a statistical evaluation of combinations of transcription factors, identified by a search algorithm running against a database of binding sites proposed for the human genome using evolutionary conservation with the mouse and rat genomes ...[more]

Dr. Stephen C. Meyer of the Discovery Institute Center for Science and Culture investigates the validity of various explanatory hypotheses for the origin of biological information, with reference to Shannon's information theory and using Dembski's complex specified information for functional biological information. Dr. Meyer's paper focuses on the surge of biological information associated with the Cambrian explosion, and refers to the informational complexity of organisms in terms of multiple layers of information from the biochemical to macroscopic and morphological levels, highlighting the explanatory power of the design hypothesis ...[more]

The Nature Publishing Group, publisher of the Nature family of scientific journals, has launched a new journal focusing specifically on providing a forum for new scientific methodologies and methods ...[more]

A group of researchers is using computational methods to predict the location and binding site composition of segmentation control elements that participate in regulating gene expression underlying the astonishing phenomena of embryonic organogenesis - that process wherein the embryos of complex life forms develop segments corresponding to the organization of the body parts of the adult organism. Applying it to the genome of the Drosophila (fruit fly), the researchers claim that their algorithm, named Ahab, based on a thermodynamic model that infers binding energies at gene binding sites and compares them to a baseline model, reinforces experimental results and increases the number of identified segmentation control elements by 50% ...[more]

An interdisciplinary team including computational biologists, geneticists and molecular biologists, working in New York and Boston, has developed an algorithm for the prediction of gene targetting by MicroRNAs (miRNAs) in the process of gene expression (transcription and translation) regulation. The algorithm depends on inter- organism evolutionary conservation principles, and the researchers have conscientiously made their algorithm and source code available as open source available for download on the internet ... [more]

Researchers studying the integration patterns of Mitochondrial DNA fragments (NUMTs) into nuclear chromosomes in humans and chimpanzees to find markers for human population genetics and evolution, have found surprising evidence that the NUMTs preferentially target coding or regulatory sequences of the human genome - especially introns and exons. They suggest that such colonization of nuclear DNA by NUMTs, as driven by environmental insults or external factors, is in fact mutagenic in nature and probably related to human disease and genetic flaws ...[more]

Researchers probe and map the intricacies of gene expression in the differentiation of retinal cells in mice, highlighting the complexity of the genomic mechanism of vertebrate retina development ...[more]

Analysis based on the completed human genome sequence suggests that different retroviruses uniquely target specific chromosomal regions for retroviral DNA integration, guided by built in 'instructions' based on chromatin features ...[more]

Newly discovered massive elliptical galaxies appear to have completed most of their development within the first 2 billion years of the proposed 14 billion year lifespan of the universe, challenging the existing heirarchical model of galaxy evolution ...[more]

French researchers have found that genetically engineered photosynthetic cyanobacteria live according to circadian rhythms, goverened by internal genetically regulated clocks. The precision of the bacteria's internal timekeeping is superior to more complex single-cell and multi-celled organisms ...[more]

Royal Truman questions the relevance of Avida simulations to neo-Darwinian evolution and pays special attention to the recent article in Nature by Lenski et. al. ...[more]

Sergei Doulatov argues that evolution is directed by functional inter-relationships in the biosphere, rather than an inherent design ...[more]

Marcus Ross reviews Simon Conway Morris' latest book - Life’s Solution: Inevitable Humans in a Lonely Universe ...[more]

Roland Hirsch discusses the Impact of forty years of advances in chemistry on evolutionary theory ... [more]

Science at the beginning of the 21st Century: which method will the scientific mainstream choose - dogma mixed with ideology or scientific analysis mixed with rational discourse?

Philosophy of Mind Issue of PCID - Volume 2.3, October 2003
The newest issue of Progress in Complexity, Information and Design features articles on non-reductive theories in the philosophy of mind. Featured authors include E.J. Lowe, Timothy O'Connor, William Hasker, Robert Koons, Todd Moody, Angus Menuge, James Barham and Micah Sparacio...[more]

ISCID was pleased to host a live chat with Lynn Caporale, author of Darwin in the Genome on Thursday November 20th. In her book, Caporale explores evolutionary mechanisms which can appear to be "startlingly strategic and purposeful" ... [more]

ISCID was pleased to host a chat with Biocosm author James N. Gardner on Thursday October 16th at 9pm Eastern titled The Selfish Biocosm Hypothesis: Intelligent Design Without a Divine Designer. Read the transcript ... [more]

ISCID was pleased to host a live online chat with cell biologist Guenter Albrecht-Buehler on Tuesday August 26th, 2003. The chat was titled: Cell Intelligence and the transcript is now online... [more].

Announcing a new book by ISCID fellow Carlos Puente, "Treasures Inside the Bell: Hidden Order in Chance" ...[more]

ISCID was pleased to host a live chat with Del Ratzsch on his latest book "Nature, Design, and Science." A transcript is now available... [more]

Announcing the The Royal Society of Chemistry's Biomolecular Dynamics and Force Generation Conference from 4-6 September 2003. The conference will highlight the investigation of biomolecular function using novel physical and chemical techniques, particularly at the single molecule level. Focus will be given to flagellar motors, DNA nanostructures and various other molecular systems...[more]

ISCID is pleased to announce the publication of the January - June 2003 Double Issue of Progress in Complexity, Information and Design. The double issue of PCID features papers from I.G.D. Strachan on evolutionary simulations, Frank J. Tipler on the nature of peer review, Joshua Smart on the application of irreducible complexity and others ...[more]

Frank J. Tipler discusses the role of peer-review in modern science as contrasted with pre-World War II refereed journals ...[more]

I.G.D. Strachan evaluates Tom Schneider's simulation and paper on the "Evolution of Biological Information" ... [more]

ISCID was pleased to host an online chat titled: Cosmic Ancestry: The Modern Version of Panspermia with panspermia theorist Brig Klyce. The transcript is now available online...[more]

David Owen asks what we can learn about algorithmic search space from a shot in the dark ...[more]

John Bracht critiques Stuart Kauffman, arguing that any general biology must incorporate the often-overlooked yet crucial role played by information in autonomous agency... [more]

Research News in Science and Theology features ISCID as their Center Spotlight for May 2003 ... [more]

The Eighteenth International Joint Conference on Artificial Intelligence will be held from August 9-15 2003 in Acapulco, Mexico and will feature key note speaker Takeo Kanade from Carnegie Mellon University...[more]

Researchers determine the crystal structure of a voltage-gated potassium channel, revealing the gating mechanism to be based on flexible, positively charged alpha-helices that extend into the hydrophobic membrane area. The arms move up or down depending on the voltage differential across the membrane, thereby opening or closing the channel....[more]

Disruption of a pseudogene was found by Hirotsune et. al. to have functional consequences in mice, and further studies revealed that the pseudogene, Makorin-p1, has a role in regulating the mRNA stability of its parent gene, Makorin....[more]

Karl D. Stephan considers whether the idea of parallel universes, discussed by Max Tegmark in the May 2003 issue of Scientific American, presents a challenge to intelligent design...[more]

A lipid raft study by Foster et.al. shows that these distinctive components of biological membranes contain large numbers of signalling proteins. ...[more]

A recent article from Tegner et. al. explores how reverse-engineering of large-scale gene networks provides insight into biological systems. ...[more]

A study of conserved residues in protein-protein binding epitopes finds that conserved polar residues are a key component of these epitopes and may be used in defining the binding surfaces....[more]

The Sante Fe Institute has appointed Dr. Robert A. Eisenstein as President effective June 1, 2003...[more]

A structural and functional study of the organic cation uptake protein, OCT1, finds that evolutionarily conserved residues have greater functional significance than other residues....[more]

In the month of July, ISCID is glad to host a month long reading discussion group on the book Nature, Design, and Science by Del Ratzsch ...[more]

ISCID encourages students to start signing up for its 2nd annual online student workshop from July 28th-August 9th. Receive a free book if you sign up by July 1st....[more]

ISCID was pleased to host UCLA Professor Jeffrey M. Schwartz in a live chat discussion titled: The Mind and the Brain...[more]

ISCID is currently looking for a self-directed college level intern. The internship will involve both self-directed research and the development of ISCID's visibility ...[more]

Dermott J. Mullan extends his discussion of the "Probability of randomly assembling a primitive cell on Earth" ... [more]

William Dembski responds to Kenneth Miller's critique of the irreducibile complexity of the bacterial flagellum ... [more]

ISCID was pleased to host University of Chicago Professor James Shapiro in a live chat discussion titled: How molecular biology opens up a 21st Century view of evolution. View the transcript ...[more]

ISCID is pleased to announce a live chat with biochemist Michael Denton in a live chat discussion titled: Protein Folds as Platonic Forms. The provisional date for the chat is April 15th, 2003. ...[more]

On Wednesday, February 5th, ISCID was pleased to host a live chat with Paul Nelson titled Ontogenetic Depth as a Complexity Metric for the Cambrian Explosion. View the transcript.