Complex Phenomena
Follow
Find
1.1K views | +0 today
 
Scooped by Colbert Sesanker
onto Complex Phenomena
Scoop.it!

Stephen Smith: 2010 Allen Institute for Brain Science Symposium

Stephen Smith, Stanford School of Medicine "Synaptic diversity: Friend or foe? Unexplained complexity at synapses.

more...
No comment yet.
Complex Phenomena
Aims to enumerate novel life science paradigms and theories. In the beginning of the twentieth century Lord Kelvin (may have) famously declared: 'There is nothing new to be discovered in physics now, All that remains is more and more precise measurement'  That was before relativity and quantum mechanics. We thought  the human genome project would unlock the workings of our bodies save a few details. Let's not make the same mistake twice. Let's explore with maniacal curiosity and critical reasoning until, truly, all that's left is refined measurement and engineering. Dedicated to the truth because pseudoscience costs lives.
Your new post is loading...
Your new post is loading...
Scooped by Colbert Sesanker
Scoop.it!

Donald E. Ingber : Wyss Institute at Harvard

Donald E. Ingber : Wyss Institute at Harvard | Complex Phenomena | Scoop.it
Donald E. Ingber is the Founding Director of the Wyss Institute for Biologically Inspired Engineering at Harvard University, the Judah Folkman Professor of Vascular Biology at Harvard Medical School and Boston Children's Hospital, and Professor of Bioengineering at the Harvard School of Engineering and Applied Sciences. He received his B.A., M.A., M.Phil., M.D. and Ph.D. from Yale University. Dr. Ingber is a founder of the emerging field of biologically inspired engineering, and at the Wyss Institute, he oversees a multifaceted effort to identify the mechanisms that living organisms use to self-assemble from molecules and cells, and to apply these design principles to develop advanced materials and devices for healthcare and to improve sustainability. He also leads the Biomimetic Microsystems platform in which microfabrication techniques from the computer industry are used to build functional circuits with living cells as components. His most recent innovation is a technology for building tiny, complex, three-dimensional models of living human organs, or "Organs on Chips", that mimic complicated human functions as a way to replace traditional animal-based methods for testing of drugs and establishment of human disease models. In addition, Dr. Ingber has made major contributions to mechanobiology, tissue engineering, tumor angiogenesis, systems biology, and nanobiotechnology. He was the first to recognize that tensegrity architecture is a fundamental principle that governs how living cells are structured to respond biochemically to mechanical forces, and to demonstrate that integrin receptors mediate cellular mechanotransduction. Dr. Ingber has authored more than 375 publications and 85 patents, and has received numerous honors including the Holst Medal, Pritzker Award from the Biomedical Engineering Society, Rous-Whipple Award from the American Society for Investigative Pathology, Lifetime Achievement Award from the Society of In Vitro Biology, and the Department of Defense Breast Cancer Innovator Award. He also serves on the Board of Directors of the National Space Biomedical Research Institute, and is a member of both the American Institute for Medical and Biological Engineering, and the Institute of Medicine of the National Academies.
Colbert Sesanker's insight:

The Ingber lab of Harvard university is leading a * revival * (note this is not new) of the solid-state and tensegrity paradigms of the cell. See below for details of these paradigms. These two paradigms are intimately related to: 

1. Models of Coherent Excitations (e.g., Frohlich's rate equation)

2. Cytoskeletal structures and the Molecules scaffolded to them. (e.g., Microtubule Network)

3. Fourth Gel phase of water discovered by Pollock. (as applied to solid-state paradigm)

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Electrodynamic eigenmodes in cellular morphology

Eigenmodes of the spherical and ellipsoidal dielectric electromagnetic resonator have been analysed. The sizes and shape of the resonators have been chosen to represent the shape of the interphase and dividing animal cell. Electromagnetic modes that have shape exactly suitable for positioning of the sufficiently large organelles in cell (centrosome, nucleus) have been identified. We analysed direction and magnitude of dielectrophoretic force exerted on large organelles by electric field of the modes. We found that the TM1m1 mode in spherical resonator acts by centripetal force which drags the large organelles which have higher permittivity than the cytosol to the center of the cell. TM-kind of mode in the ellipsoidal resonator acts by force on large polarizable organelles in a direction that corresponds to the movement of the centrosomes (also nucleus) observed during the cell division, i.e. to the foci of the ellipsoidal cell.

Minimal required force (10−16 N), gradient of squared electric field and corresponding energy (10−16 J) of the mode have been calculated to have biological significance within the periods on the order of time required for cell division. Minimal required energy of the mode, in order to have biological significance, can be lower in the case of resonance of organelle with the field of the cellular resonator mode.

In case of sufficient energy in the biologically relevant mode, electromagnetic field of the mode will act as a positioning or steering mechanism for centrosome and nucleus in the cell, thus contribute to the spatial and dynamical self-organization in biological systems.
Colbert Sesanker's insight:

Models the cell as ellipsoidal dielectric electromagnetic resonator and argues the positioning of organelles corresponds to eigenmodes. Cellular cavity structures could function as waveguides and resonators and  membrane bound organelles could impose necessary boundary conditions. In other words membrane bound structures are proposed to be optimally positioned.  Not a new idea, but these simulations offer more support.

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

The Fourth Phase of Water: Dr. Gerald Pollack at TEDxGuelphU - YouTube

Does water have a fourth phase, beyond solid, liquid and vapor?

University of Washington Bioengineering Professor Gerald Pollack answers this question, and intrigues us to consider the implications of this finding. Not all water is H2O, a radical departure from what you may have learned from textbooks.

Pollack received his PhD in biomedical engineering from the University of Pennsylvania in 1968. He then joined the University of Washington faculty and is now professor of Bioengineering. His interests have ranged broadly, from biological motion and cell biology to the interaction of biological surfaces with aqueous solutions. His 1990 book, Muscles and Molecules: Uncovering the Principles of Biological Motion, won an "Excellence Award" from the Society for Technical Communication; his more recent book, Cells, Gels and the Engines of Life, won that Society's "Distinguished Award." Pollack received an honorary doctorate in 2002 from Ural State University in Ekaterinburg, Russia, and was more recently named an Honorary Professor of the Russian Academy of Sciences. He received the Biomedical Engineering Society's Distinguished Lecturer Award in 2002. In 2008, he was the faculty member selected by the University of Washington faculty to receive their highest annual distinction: the Faculty Lecturer Award. Pollack is a Founding Fellow of the American Institute of Medical and Biological Engineering and a Fellow of both the American Heart Association and the Biomedical Engineering Society. He is also Founding Editor-in-Chief of the journal, WATER, and has recently received an NIH Transformative R01 Award. He was the 2012 recipient of the Prigogine Medal and in 2013 published his new book: The Fourth Phase of Water: Beyond Solid, Liquid, and Vapor.
Colbert Sesanker's insight:

Tensegrity, cytosociology and the gel like phase of water all contribute to the long held hypothesis that the cell is a solid state structure (see Tensegrity below).

 

 

Frohlich proposed the 'microtrabecular lattice' as the substrate of energy transfer for coherent excitations in the early 80s. The microtrabecular lattice idea WAS an artifact of early HVEM during this time. Interestingly, a solid-state cell would support coherent excitations of polar molecules (cell is saturated with these) and membranes across multiple frequency bands. Indeed, it is a new and improved revitalization of the microtrabecular concept. 

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Pollack Laboratory - Water and Cell Biology

Pollack Laboratory - Water and Cell Biology | Complex Phenomena | Scoop.it
The book, Cells, Gels and the Engines of Life builds on the central role of water for biology. It provides evidence that much of the water in the cell is very near to one or another hydrophilic surface and therefore ordered, and that cell behavior can be properly understood only if this feature is properly taken into account. It goes on to show that seemingly complex behaviors of the cell can be understood in simple terms once a proper understanding of water and surfaces is achieved.

While the book is an award-winning best seller, it has aroused controversy because it questions some long-held basic features of cell function such as membrane channels and pumps. This steps on many scientific toes. Many others have praised the insights obtained from building on a foundation of first principles (see book website above). One prominent reviewer from Harvard University opines that the book is “a 305 page preface to the future of cell biology.”
Colbert Sesanker's insight:

further details solid state cell paradigm. Reads like a childrens book in a good way (super clear and non-technical).

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Ingber Lab

Ingber Lab | Complex Phenomena | Scoop.it
Cellular Tensegrity Theory. Cells and tissues are organized as discrete network structures, and they use tensegrity architecture to mechanically stabilize themselves. In the cellular tensegrity theory, complex mechanical behaviors in cells and tissues emerge through establishment of a mechanical force balance between different molecular elements in the cytoskeleton and ECM that maintains the cell in a state of isometric tension.

Solid-State Biochemistry. Many of the biochemical events that mediate cell metabolism and signal transduction proceed using solid-state biochemistry. The enzymes and substrates that mediate these biochemical reactions are physically immobilized on insoluble molecular scaffolds within the cytoskeleton, nucleus and ECM.

Integrins as Mechanotransducers. Mechanical forces impact cellular signal transduction and influence cell decision making based on their transmission across cell surface adhesion receptors, such as integrins, that mechanically couple extracellular molecular scaffolds to the internal cytoskeleton. Mechanical forces are converted into chemical and electrical signals through stress-dependent distortion of molecules that associate with load-bearing elements of the cytoskeleton.
more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

On the "cytosociology" of enzyme action in vivo: a novel thermodyna... - PubMed - NCBI

J Theor Biol. 1981 Dec 21;93(4):701-35.
Colbert Sesanker's insight:

The idea here is that an enzyme stripped of its 'cytosociology' is merely a shadow of its identity. It's naturally highly diverse environment is the key to its functioning. Offers more support for the solid state view of the cell.

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Whatever happened to the ‘microtrabecular concept’? - Heuser - 2012 - Biology of the Cell - Wiley Online Library

Keith Porter culminated his stellar career as the founding father of biological electron microscopy by acquiring, in the late 1970s, a high-voltage electron microscope (HVEM). With this magnificent instrument he examined whole-mounts of cultured cells, and perceived within them a structured cytoplasmic matrix he named the “microtrabecular lattice”. Over the next decade Porter published a series of studies, together with a team of outstanding young colleagues, which elaborated his broader “microtrabecular concept.” This concept posited that microtrabeculae were real physical entities that represented the fundamental organization the cytoplasm, and that they were the physical basis of cytoplasmic motility and of cell-shape determination. The present review presents Porter's original images of microtrabeculae, after conversion to a more interpretable “digital-anaglyph” form, and discusses the rise and fall of the microtrabecular concept. Further, it explains how the HVEM images of microtrabeculae finally came to be considered as an artifact of the preparative methods Porter used to prepare whole cells for HVEM. Still, Keith's “microtrabecular concept” foretold of our current appreciation of the complexity and pervasiveness of the cytoskeleton, which has now been found by more modern methods of EM to actually be the fundamental organizing principle of the cytoplasmic matrix. During the impending eclipse of Porter's microtrabecular concept in the late 1980s, many of Keith's colleagues fondly described the cell as being filled, not with protoplasm, but with “Porterplasm.” Despite the fact that Keith's view was clouded by the methods of his time, it would be fitting and apt to retain this name, still today, for the ordered matrix of cytoskeletal macromolecules that exists in the living cell. In the end, the story of what happened to Porter's microtrabecular concept should be an object lesson in scientific hubris that should humble and inform all of us in cell biology, even today — particularly when we begin to think that our most recent methods and observations are achieving “the last word”.
Colbert Sesanker's insight:

frohlich proposed this lattice as the substrate of energy transfer for coherent excitations in the early 80s. Interestingly, the microtrabecular lattice idea WAS an artifact of early HVEM during this time. Originally proposed for the medium of excitations before the solid state conception solidified. 

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Nutritional Control of Reproductive Status in Honeybees via DNA Methylation

Nutritional Control of Reproductive Status in Honeybees via DNA Methylation | Complex Phenomena | Scoop.it

"Fertile queens and sterile workers are alternative forms of the adult female honeybee that develop from genetically identical larvae following differential feeding with royal jelly. We show that silencing the expression of DNA methyltransferase Dnmt3, a key driver of epigenetic global reprogramming, in newly hatched larvae led to a royal jelly–like effect on the larval developmental trajectory; the majority of Dnmt3 small interfering RNA–treated individuals emerged as queens with fully developed ovaries. Our results suggest that DNA methylation in Apis is used for storing epigenetic information, that the use of that information can be differentially altered by nutritional input, and that the flexibility of epigenetic modifications underpins, profound shifts in developmental fates, with massive implications for reproductive and behavioral status."

Colbert Sesanker's insight:

 The bee colony is genetically identical, but Queens are made when workers feed larva 'Royal Jelly' for an extended period of time. Queens exhibit vastly different gene expression patterns from workers. This is caused by epigenetic modifications. 


The queen differentiation program was replicated by blocking (using small siRNA to silence methyltransferase Dnmt3) CpG methylation in larva.

 

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Effects of the gut microbiota on bone mass: Trends in Endocrinology & Metabolism

Effects of the gut microbiota on bone mass: Trends in Endocrinology & Metabolism | Complex Phenomena | Scoop.it
Studies in germ-free (GF) mice demonstrate that the gut microbiota (GM) is a regulator of bone mass.The GM affects bone mass via effects on the immune status, which in turn regulates osteoclastogenesis.Probiotic and prebiotic treatments may impact GM composition and affect bone metabolism.The GM may be a novel therapeutic target for osteoporosis.

 

The gut microbiota (GM), the commensal bacteria living in our intestine, performs numerous useful functions, including modulating host metabolism and immune status. Recent studies demonstrate that the GM is also a regulator of bone mass and it is proposed that the effect of the GM on bone mass is mediated via effects on the immune system, which in turn regulates osteoclastogenesis. Under normal conditions, the skeleton is constantly remodeled by bone-forming osteoblasts (OBs) and bone-resorbing osteoclasts (OCLs), and imbalances in this process may lead to osteoporosis. Here we review current knowledge on the possible role for the GM in the regulation of bone metabolism and propose that the GM might be a novel therapeutic target for osteoporosis and fracture prevention.

 

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

A Flood of Borrowed Genes at the Origins of Tiny Extremists – Phenomena: Not Exactly Rocket Science

A Flood of Borrowed Genes at the Origins of Tiny Extremists – Phenomena: Not Exactly Rocket Science | Complex Phenomena | Scoop.it
The team then looked at the other 12 lineages and found exactly the same pattern. The origin of every major archaeal group was marked by the acquisition of bacterial genes—sometimes dozens, sometimes thousands. They borrowed, then they branched out. “The implication here is that such transfers played an important role in the actual establishment of the groups themselves,” says John Archibald from Dalhousie University.

“It was a surprise for us,” says Bill Martin from Heinrich-Heine University in Dusseldorf, who led the study. “You might ask why no one else has seen this before.” It’s probably because most scientists focused on the essential “core genes” that are common to all archaea. But the core genes comprise just 1 percent of the genome. They can tell us the shape of the archaeal family tree, but they say nothing about the characteristics that define the branches. To do that, you need to look at the entire genome, which is exactly what Nelson-Sathi did.

The “horizontal gene transfers” that he found are alien to us humans, who can only pass genes from parent to child. But bacteria and archaea don’t suffer the yoke of vertical inheritance. They can pass genes to one another with great ease.

These transfers could flow in either direction but in reality, they were mostly one-way. Nelson-Sathi found that bacteria have donated gene families to archaea five times more frequently than vice versa, and none of the archaea-to-bacteria transfers correspond to the rise of major bacterial groups. Bacteria have repeatedly thrust their archaeal peers into new evolutionary directions, but the reverse isn’t true.
more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Action-at-a-distance interactions enhance protein binding affinity

"An alternative strategy that does not demand the same detailed packing of side chains into an exquisite three-dimensional jigsaw puzzle may be desirable in many cases. One such method involves the enhancement of affinity through relatively long-range electrostatic effects by the mutation of surface residues located somewhat outside of the binding interface. When surface mutations are not located directly at the binding interface, a detailed consideration of packing may be unnecessary. Moreover, when the effects of mutations act over a relatively long range, such as through electrostatic interactions, design attributes should be more tolerant of local imperfections in structural models. Less apparent, however, is how effective these types of mutations can be (since much of the interaction may be screened by solvent), and how particularly favorable mutations of this class can be identified. An important design consideration is the counterplay of favorable intermolecular electrostatic interactions made between the partners in the bound state and unfavorable desolvation costs incurred by each partner due to binding; this balance leads to counterintuitive behavior for the energetics of electrostatic interactions in biological systems (e.g., Hendsch and Tidor 1994 e.g., Hendsch and Tidor 1999; Lee and Tidor 1997). ".

Colbert Sesanker's insight:

Enzymes attract their substrates in a frequency specific manner at a distance. This idea is very old and described in the 'Theoretical Physics and Biology' section of' Biological Coherence and Response to External Stimuli ' from 1988.

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Could Humans Recognize Odor by Phonon Assisted Tunneling?

Could Humans Recognize Odor by Phonon Assisted Tunneling? | Complex Phenomena | Scoop.it
Our sense of smell relies on sensitive, selective atomic-scale processes that occur when a scent molecule meets specific receptors in the nose. The physical mechanisms of detection are unclear: odorant shape and size are important, but experiment shows them insufficient. One novel proposal suggests receptors are actuated by inelastic electron tunneling from a donor to an acceptor mediated by the odorant, and provides critical discrimination. We test the physical viability of this mechanism using a simple but general model. With parameter values appropriate for biomolecular systems, we find the proposal consistent both with the underlying physics and with observed features of smell. This mechanism suggests a distinct paradigm for selective molecular interactions at receptors (the swipe card model): recognition and actuation involve size and shape, but also exploit other processes.
Colbert Sesanker's insight:

more corroboration of luca turin's vibrational theory of smell

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

A Quantum of Solace - Molecular Electronics of Benzodiazepines (Google Workshop on Quantum Biology) - YouTube

"Benzodiazepines and related drugs modulate the activity of GABA-A receptors, the main inhibitory receptor of the central nervous system. The prevailing view is that these drugs bind at the interface between two receptor subunits and allosterically modulate the response to GABA. In this talk I shall present evidence that benzodiazepines work instead by facilitating electron transport from the cytoplasm to a crucial redox-sensitive group in the gamma subunit. If this idea is correct, benzodiazepines should not only be regarded as keys fitting into a lock, but also as one-electron chemical field-effect transistors fitting into an electronic circuit. "

Colbert Sesanker's insight:

Luca Turin describing benzodiazepines binding to GABA-A receptors via resonance. Similar to his theory of smell. Distinct from the lock and key model.  

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Guenter Albrecht-Buehler: Publications

Guenter Albrecht-Buehler: Publications | Complex Phenomena | Scoop.it

Mechanisms of information processing in single cells

 

Colbert Sesanker's insight:

Guenter Albrecht-Buehler spent 30 years studying information processing in single cells. He has accumulated substantial evidence that individual eukaryotic cells can  respond to a variety of electromagnetic and mechanical stimuli,  perform sophisticated calculations on this sensory data and respond appropriately.

Centriole structures are proposed  as the sensory apparatus for electromagnetic data acquisition and cytoskeletal structures, e.g., microtubules, serve as the structures that process the sensory data.

The cytoskeleton, elaborated in the  cellular tesengrity paradigm (see Ingber lab below for details) processes the mechanical information.

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Cellular memory hints at the origins of intelligence : Nature News

Cellular memory hints at the origins of intelligence : Nature News | Complex Phenomena | Scoop.it
Like all living organisms, slime moulds have built-in biochemical oscillators, like the human body clock. In other kinds of slime mould, these oscillators can create periodic ripple patterns in response to environmental stress, helping the organism coordinate its movements. Nakagaki's group thinks that the versatile rhythmic sense of Physarum stems from many different biochemical oscillators in the colony operating at a continuous range of frequencies.

The team's calculations show that such a group of oscillators can pick up and 'learn' any imposed rhythmic beat, although the knowledge decays quickly once stimulus ceases. The calculations also show that a memory of the beat can stay within the system, and be released again by a single, later pulse — just as the researchers observed. 
Colbert Sesanker's insight:

With regards to accumulated experimental evidence, efficiency and stability of computation (stable read write, not biochemical currents), Guenter Albrecht-Buehler's 30 years of research proposing cytoskeletal structures like centrioles and microtubule lattices for this type of computation is much more convincing. Indeed such structures are proposed for MUCH more complicated forms of information processing and should certainly be taken into consideration.

"In my view, simulation is not an adequate approach for such a deep biological problem as intelligence," says Guenter Albrecht-Buehler at Northwestern University Medical School in Chicago. "We need to find out how it's really done in a living cell." He points out that all sorts of electronic models could have simulated genetic memory but wouldn't have helped to understand how cells achieve that particular trick. "Finding the double helix of DNA was the only achievement that really mattered," he says.

Here he is cleverly hinting at cytoskeletal structures as the next DNA.  

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Pollack Laboratory - Pollack Laboratory

Pollack Laboratory - Pollack Laboratory | Complex Phenomena | Scoop.it

"Water has three phases – gas, liquid, and solid; but recent findings from our laboratory imply the presence of a surprisingly extensive fourth phase that occurs at interfaces. This finding may have unexpectedly profound implication for chemistry, physics and biology."

 

"Water and Cell Biology:
Contemporary views of cell biology consider water merely as a background carrier of the more important molecules of life. However, water may be a central player in life processes."

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Tensegrity and Complex Systems Biology

Tensegrity and Complex Systems Biology | Complex Phenomena | Scoop.it

"Importantly, working with collaborators, such as Drs. Ning Wang (Dept. of Respiratory Biology, Harvard School of Public Health) and Dimitrije Stamenovic (Dept. of Biomedical Engineering, Boston U.), we have been able to demonstrate that living mammalian cells behave mechanically like tensegrity structures. Moreover, we have developed a theoretical formulation of the tensegrity model starting from first mechanical principles that has yielded accurate qualitative and quantitative predictions of many static and dynamic cell mechanical behaviors. We are currently trying to extend and strengthen this computational approach to explain systems-wide mechanical properties in mammalian cells, and to explore their hierarchical basis

 

 

The cellular tensegrity model proposes that the whole cell is a prestressed tensegrity structure, although geodesic structures are also found in the cell at smaller size scales (e.g. clathrin-coated vesicles, viral capsids). In the model, tensional forces are borne by cytoskeletal microfilaments and intermediate filaments, and these forces are balanced by interconnected structural elements that resist compression, most notably internal microtubule struts and ECM adhesions. However, individual filaments can have dual functions and hence bear either tension or compression in different structural contexts or at different size scales (e.g. contractile microfilaments generate tension, whereas actin microfilament bundles that are rigidified by cross-links bear compression in filopodia). The tensional prestress that stabilizes the whole cell is generated actively by the contractile actomyosin apparatus. Additional passive contributions to this prestress come from cell distension through adhesions to the ECM and other cells, osmotic forces acting on the cell membrane, and forces exerted by filament polymerization. Intermediate filaments that interconnect at many points along microtubules, microfilaments and the nuclear surface provide mechanical stiffness to the cell based on their material properties and on their ability to act as suspensory cables that interconnect and tensionally stiffen the entire cytoskeleton and nuclear lattice."

 

Colbert Sesanker's insight:

The solid state view of the cell where enzymes and substrates that mediate biochemical reactions are physically immobilized and secured on cytoskeletal scaffolds, the ECM and organelles would supply a suitable medium for coherent excitations.

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

tensegrity - Ingber, Donald A

tensegrity - Ingber, Donald A | Complex Phenomena | Scoop.it

"Due to his work, the cytoskeleton is now widely believed to be a tensegrity structure, and tensegrity mechanics at the cellular level is now close to replacing all previous mechanical models of the cell."

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

The Histone Code: Judd Rice Laboratory at the USC/Norris Comprehensive Cancer Center

The Histone Code: Judd Rice Laboratory at the USC/Norris Comprehensive Cancer Center | Complex Phenomena | Scoop.it

"Increasing evidence indicates that the post-translationally modified histones serve as extremely selective binding platforms for specific regulatory proteins that drive distinct nuclear processes.

It has been known for over 45 years now that histones can be post-translationally modified by specific enzymes that ‘write?a histone code by adding or removing a number of different chemical modifications, including acetyl, phosphoryl and methyl groups (Figure 2). Since these modifications occur only on specific amino acid residues on specific histones in various eukaryotic organisms, these observations strongly linked the modifications?involvement in nuclear processes. For example, the acetylation of key lysine residues of histone H3 and H4 by enzymes known as histone acetyltransferases (HATs) was known to play a pivotal role in transcriptional activation." 

 

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Royal jelly - Wikipedia, the free encyclopedia

Royal jelly

Royal jelly is a honey bee secretion that is used in the nutrition of larvae, as well as adult queens. It is secreted from the glands in the hypopharynx of worker bees, and fed to all larvae in the colony, regardless of sex or caste.

"The honey bee queens and workers represent one of the most striking examples of environmentally controlled phenotypic polymorphism. In spite of their identical clonal nature at the DNA level, they are strongly differentiated across a wide range of characteristics including anatomical and physiological differences, longevity of the queen, and reproductive capacity.[6] Queens constitute the sexual caste and have large active ovaries, whereas workers have only rudimentary, inactive ovaries and are functionally sterile. The queen/worker developmental divide is controlled epigenetically by differential feeding with royal jelly; this appears to be due specifically to the protein royalactin. A female larva destined to become a queen is fed large quantities of royal jelly; this triggers a cascade of molecular events resulting in development of a queen.[3] It has been shown that this phenomenon is mediated by an epigenetic modification of DNA known as CpG methylation.[7] Silencing the expression of an enzyme that methylates DNA in newly hatched larvae led to a royal jelly-like effect on the larval developmental trajectory; the majority of individuals with reduced DNA methylation levels emerged as queens with fully developed ovaries. This finding suggests thatDNA methylation in honey bees allows the expression of epigenetic information to be differentially altered by nutritional input."

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Gut–brain link grabs neuroscientists

Gut–brain link grabs neuroscientists | Complex Phenomena | Scoop.it

"Scientists were shocked to learn that about 90 percent of the fibers in the primary visceral nerve, the vagus, carry information from the gut to the brain and not the other way around."

 

"The enteric nervous system uses more than 30 neurotransmitters, just like the brain, and in fact 95 percent of the body's serotonin is found in the bowels."

 

 

Colbert Sesanker's insight:

Was there any reason to assume no link?  

 

"The second brain doesn't help with the great thought processes…religion, philosophy and poetry is left to the brain in the head," says Michael Gershon, chairman of the Department of Anatomy and Cell Biology at New York–Presbyterian Hospital/Columbia University Medical Center, an expert in the nascent field of neurogastroenterology and author of the 1998 book The Second Brain"

 

Somehow he 'knows' the gut 'doesn't help' with higher order cognitive reasoning.  Even if the gut served as a switch to initiate different cognitive programs, that would certainly constitute 'help' and seems plausible. Indeed, if there is feedback between the gut and higher order cognition, one would have to accept the gut is part of the system mediating the higher order cognition.

 

 

 

 

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Machine-Learning Maestro Michael Jordan on the Delusions of Big Data and Other Huge Engineering Efforts - IEEE Spectrum

Machine-Learning Maestro Michael Jordan on the Delusions of Big Data and Other Huge Engineering Efforts - IEEE Spectrum | Complex Phenomena | Scoop.it

"Why We Should Stop Using Brain Metaphors When We Talk About Computing.

 

Spectrum: It’s always been my impression that when people in computer science describe how the brain works, they are making horribly reductionist statements that you would never hear from neuroscientists. You called these “cartoon models” of the brain.

 

Michael Jordan: I wouldn't want to put labels on people and say that all computer scientists work one way, or all neuroscientists work another way. But it’s true that with neuroscience, it’s going to require decades or even hundreds of years to understand the deep principles. There is progress at the very lowest levels of neuroscience. But for issues of higher cognition—how we perceive, how we remember, how we act—we have no idea how neurons are storing information, how they are computing, what the rules are, what the algorithms are, what the representations are, and the like. So we are not yet in an era in which we can be using an understanding of the brain to guide us in the construction of intelligent systems."

Colbert Sesanker's insight:

finally someone calls out the lost that think the brain is one giant deep neural network or (gasp) a hierarchical hidden markov model (kurzweil in 'How to Build a Mind'). 'What is thought', by Eric Baum, is another excellent book summarizing materialistic (computational and evolutionary) views of intelligence (though I think it's optimism on the feasibility of strong AI is in error).

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

How Jetlag Disrupts The Ticks of Your Microbial Clock – Phenomena: Not Exactly Rocket Science

How Jetlag Disrupts The Ticks of Your Microbial Clock – Phenomena: Not Exactly Rocket Science | Complex Phenomena | Scoop.it

"Your genome is the same right now as it was yesterday, last week, last year, or the day you were born. But your microbiomes—the combined genes of all the trillions of microbes that share your body—have shifted since the sun came up this morning. And they will change again before the next sunrise.

Christoph Thaiss from the Weizmann Institute of Science has discovered that the communities of microbes in out guts vary on a daily cycle. Some species rise to the fore during daylight hours and recede into the background at night, while others show the opposite pattern.

These cycles are a lot like our own body clocks, or circadian rhythms. Over a 24 hour period, the levels of many molecules in our body rise and fall in predictable fashion. These rhythms affect everything from our body temperature to our brain activity to how well we respond to medicine. But these clocks tick by themselves. You can reset them by exposing yourself to light at different times of day (which is what we do when we cross time zones and get jetlag), but they are still self-sustaining.

Our microbiome clock is not. The microbes aren’t waxing and waning of their own accord. Their world is completely dark. There’s no way for them to tell what time of the day it is, except for clues provided by us. The most important of these clues is food. Thanks to our own rhythms, we eat at regular times of the day, and it’s these feeding patterns that drive the cycles in our microbiome. Diet is the gear that synchronises the ticks of our clocks with those of our microbes."

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

The investigation of the effects of counterions in protein dynamics simulations

Electrostatic effects not only play an important role in stabilizing proteins' compact structures (Wada and Nakamura, 1981) but the specificity of structure recognition is also determined to a significant extent by electrostatics (Nakamura and Wada, 1985; Jug and Gerwens, 1998).
Colbert Sesanker's insight:

Intimately related to coherent excitations as these can excite proteins and increase their affinities toward their substrates 

more...
No comment yet.
Scooped by Colbert Sesanker
Scoop.it!

Flies sniff out heavy hydrogen : Nature News

Flies sniff out heavy hydrogen : Nature News | Complex Phenomena | Scoop.it
Skoulakis and his colleagues say that the results offer strong support to a controversial theory of how olfaction works; a theory proposed previously by one of the report's co-authors, Luca Turin at the Massachusetts Institute of Technology in Cambridge. According to Turin, odorants are identified not according to their molecular shape, but their atomic vibrations.

"This is an important paper, and offers very strong evidence in favour of the vibrational theory of olfaction," says materials physicist Andrew Horsfield of Imperial College London.
Colbert Sesanker's insight:

corroboration of luca turin's vibration theory of smell

more...
No comment yet.