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Scientists identify viral gene driving sick gypsy moth caterpillars to climb high and die

Scientists identify viral gene driving sick gypsy moth caterpillars to climb high and die | Modern Biology | Scoop.it
For a century, scientists have watched European gypsy moth caterpillars infected with a virus use their last strength to do something that a healthy gypsy moth caterpillar would never do in daylight hours -- climb high into a tree and onto a leaf.
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Modern Biology
This collection spans from (8 / 2012) - (present).9 pages. Completed by 4/ 3/ 2017. Correction, by 9 / 2017 (date changed 5/ 18/ 2016), New version on paper in 2018.  All pages are updated weekly with related articles grouped, so new stuff may be on any page. --Colbert
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Stephen Wolfram: 'Can We Really Be the Smartest Things in the Universe? | Inc. Magazine

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Colbert Sesanker's insight:
The summit of the computational paradigm. In summary, computational history, with all its details and particulars, not computation itself its what's important. The entire time indexed process. 
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The Fourth Phase of Water: Dr. Gerald Pollack (University of Washington)

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), a liquid crystal

 

 

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. In this sense, it is an updated version of the microtrabecular concept. 


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ORNL researchers discover a new state of water molecule

Neutron scattering and computational modeling have revealed unique and unexpected behavior of water molecules under extreme confinement that is unmatched by any known gas, liquid or solid states. Read more
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Ingber Lab (Harvard)

Ingber Lab (Harvard) | Modern Biology | 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.
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tensegrity - Ingber, Donald A

tensegrity - Ingber, Donald A | Modern Biology | 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."

Colbert Sesanker's insight:

There is a lot of room to test these ideas computationally. Also, this design principle could inspire new tensegrity designs in engineering

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Donald E. Ingber : Wyss Institute at Harvard

Donald E. Ingber : Wyss Institute at Harvard | Modern Biology | 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 studies the solid-state and tensegrity paradigms of the cell. See below for details of these paradigms. These two paradigms may be 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)

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High-frequency electric field and radiation characteristics of cellular microtubule network (Journal of Theoretical Biology)

High-frequency electric field and radiation characteristics of cellular microtubule network (Journal of Theoretical Biology) | Modern Biology | Scoop.it
Microtubules are important structures in the cytoskeleton, which organizes the cell. Since microtubules are electrically polar, certain microtubule normal vibration modes efficiently generate oscillating electric field. This oscillating field may be important for the intracellular organization and intercellular interaction. There are experiments which indicate electrodynamic activity of variety of cells in the frequency region from kHz to GHz, expecting the microtubules to be the source of this activity. In this paper, results from the calculation of intensity of electric field and of radiated electromagnetic power from the whole cellular microtubule network are presented. The subunits of microtubule (tubulin heterodimers) are approximated by elementary electric dipoles. Mechanical oscillation of microtubule is represented by the spatial function which modulates the dipole moment of subunits. The field around oscillating microtubules is calculated as a vector superposition of contributions from all modulated elementary electric dipoles which comprise the cellular microtubule network. The electromagnetic radiation and field characteristics of the whole cellular microtubule network have not been theoretically analyzed before. For the perspective experimental studies, the results indicate that macroscopic detection system (antenna) is not suitable for measurement of cellular electrodynamic activity in the radiofrequency region since the radiation rate from single cells is very low (lower than 10−20 W). Low noise nanoscopic detection methods with high spatial resolution which enable measurement in the cell vicinity are desirable in order to measure cellular electrodynamic activity reliably.
Colbert Sesanker's insight:

Get the paper here: https://drive.google.com/open?id=0B2tdeG58s2pBd1V3UGUtM0lXSWM

Solid State Biology reading List here: https://drive.google.com/open?id=0B2tdeG58s2pBRHlrM0tYc0poU1k

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Multi-level memory-switching properties of a single brain microtubule (Applied Physics Letters)

We demonstrate that a single brain-neuron-extracted microtubule is a memory-switching element, whose hysteresis loss is nearly zero. Our study shows how a memory-state forms in the nanowire and how its protein arrangement symmetry is related to the conducting-state written in the device, thus, enabling it to store and process ∼500 distinct bits, with 2 pA resolution between 1 nA and 1 pA. Its random access memory is an analogue of flash memory switch used in a computer chip. Using scanning tunneling microscope imaging, we demonstrate how single proteins behave inside the nanowire when this 3.5 billion years old nanowire processes memory-bits.
Colbert Sesanker's insight:

Anirban Bandyopadhyay is an author

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Jack Tuszynski: Coherence in Biology Part II Winter 2015 (University of Alberta)

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How a Cat Parasite Affects Your Behavior, Mental Health, and Sex Drive

How a Cat Parasite Affects Your Behavior, Mental Health, and Sex Drive | Modern Biology | Scoop.it

"Parasitic mind-control is common in the animal kingdom. The rabies virus produces a delirious rage in its dying host, causing the animal to infect new victims with its bite. The hairworm Spinochordodes tellinii manipulates the brains of crickets into committing suicide by leaping into water, where the worm can breed. When the protozoanToxoplasma gondii enters a rodent, the animal’s natural fear of cat urine is reversed. The rodent becomes attracted to the odor of its predator, and when eaten, the parasite is able to spawn inside the feline’s intestines.
 

Although Toxoplasma is primarily a rodent parasite, human beings are not immune. Our cohabitation with cats ensures ample opportunity for toxoplasmosis to occur through fecal contact. Since its discovery in the early 1900s, the protozoan had been widely viewed as a relatively benign passenger in humans. The only perceived threat was to patients with compromised immune systems (such as people with AIDS) and pregnant women whose fetuses are often deformed or aborted by the pathogen. It was believed that a healthy human host could control the parasite indefinitely. New evidence suggests the opposite. Through a delicate finessing of the neurotransmitters in our brains, it is us who are being controlled. "

 

 

Colbert Sesanker's insight:

wouldn't be surprised if they were a lot more of these with complex life cycles that make them more difficult to detect. They are many 'stories' on the toxo life cycle, anthropomorphised with with intentions, desires, personalities  ... but mainly contradictions (just look at some other descriptions of how it influences male behavior).  There's no reason to frame it in this type of story to begin with.

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Coexisting Stable Equilibria in a Multiple-allele Population Genetics Model

In this paper we find and classify all patterns for a single locus three- and four-allele population genetics models in continuous time. A pattern for a k-allele model means all coexisting locally stable equilibria with respect to the flow defined by the equations p˙i=pi(ri−r),i=1,...,k, where pi,ri are the frequency and marginal fitness of allele Ai, respectively, and r is the mean fitness of the population. It is well known that for the two-allele model there are only three patterns depending on the relative fitness between the homozygotes and the heterozygote. It turns out that for the three-allele model there are 14 patterns and for the four-allele model there are 117 patterns. With the help of computer simulations, we find 2351 patterns for the five-allele model. For the six-allele model, there are more than 60,000 patterns. In addition, for each pattern of the three-allele model, we also determine the asymptotic behavior of solutions of the above system of equations as t→∞. The problem of finding patterns has been studied in the past and it is an important problem because the results can be used to predict the long-term genetic makeup of a population.
Colbert Sesanker's insight:

Three player game with all coexisting strategies enumerated (not necessarily Nash Equilibria). Population frequencies governed by replicator equation. Higher player games considered  using simulations (up to n = 6).

 

This came out of my undergraduate senior thesis. Our claim that this is an 'evolutionary model'  isn't quite right

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Gene drives spread their wings (Science News)

Gene drives spread their wings (Science News) | Modern Biology | Scoop.it
Gene drive enthusiasts say these genies could wipe out malaria, saving more than half a million lives each year. Invasive species, herbicide-resistant weeds and pesticide-resistant bugs could be driven out of existence. Animals that carry harmful viruses could be immunized with ease.

Scientists have sought the power of gene drives for decades. But only with the emergence of a genetic tool called CRISPR/Cas9 — the bottle opener that unleashed the genie — has gene drive technology offered the prospect of providing a speedy means to end some of the world’s greatest health and ecological scourges.
Colbert Sesanker's insight:
We modeled this last summer:

 https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxjb2xiZXJ0c2VzYW5rZXJyZXNlYXJjaHxneDoxZjA2NTNmOTA5Mjk1ZDI1

Use the ideas here to build predictive models for the Zika virus
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Statistical physics of self-replication (The Journal of Chemical Physics)

Self-replication is a capacity common to every species of living thing, and simple physical intuition dictates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous and quantitative by deriving a lower bound for the amount of heat that is produced during a process of self-replication in a system coupled to a thermal bath. We find that the minimum value for the physically allowed rate of heat production is determined by the growth rate, internal entropy, and durability of the replicator, and we discuss the implications of this finding for bacterial cell division, as well as for the pre-biotic emergence of self-replicating nucleic acids.
Colbert Sesanker's insight:
Irreversibility. Irreversibility. Irreversibility. The defining feature of life and you know what else, I won't use the word here.
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What is life-lecture: Gerald H. Pollack (University of Washington)

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University of Washington: Pollack Laboratory - Pollack Laboratory

University of Washington: Pollack Laboratory - Pollack Laboratory | Modern Biology | 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."

Colbert Sesanker's insight:

In particular the highly structured 4th phase of water present in the cell can lower the viscous damping of vibrating molecules (e.g., proteins).

 

organisms really are like bags of water if you think about it

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Pollack Laboratory - Water and Cell Biology

Pollack Laboratory - Water and Cell Biology | Modern Biology | 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:

Reads like a children's book in a good way (super clear and non-technical). Describes a novel 4th phase of water and biological implications.

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Tensegrity and Complex Systems Biology (Harvard)

Tensegrity and Complex Systems Biology (Harvard) | Modern Biology | 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:

Of particular interest is 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.

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Journal of Theoretical Biology (1981): On the "cytosociology" of enzyme action in vivo: a novel thermodynamic correlate of biological evolution

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. 

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Does a cell perform isoelectric focusing?

A model of intracellular electrical sorting of enzymes and organelles in the cytosol, based on isoelectric focusing, is proposed. The focusing is suggested to take place over a centrally symmetric pH gradient which in the cytosol of the yeast Saccharomyces cerevisiae is known to be 7.2-6.4. From published data on the energetic capacity and from the computed electric resistance of the S. cerevisiae cell, the maximum value of the electric field that can be maintained in the cytosol was estimated. The results showed that the strength of a centrally symmetric intracytosolic electric field could be as high as 90 mV/cm, which is sufficient to account for sorting of cytosolic proteins according to their isoelectric points. Although direct experimental evidence for intracellular isoelectric focusing is still missing, several phenomena of physiological importance can be understood on the assumption of its real existence.
Colbert Sesanker's insight:

found this one after digging through Jaroslav Flegr's papers on Toxoplasmosis.

Frohlich made a small enzyme kinetics model of this idea on page 12 of his green book from 1988

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An organic jelly made fractal logic gate with an infinite truth table : (Nature, Scientific Reports)

An organic jelly made fractal logic gate with an infinite truth table : (Nature,  Scientific Reports) | Modern Biology | Scoop.it

Widely varying logic gates invented over a century are all finite. As data deluge problem looms large on the information processing and communication industry, the thrust to explore radical concepts is increasing rapidly. Here, we design and synthesis a molecule, wherein, the input energy transmits in a cycle inside the molecular system, just like an oscillator, then, we use the molecule to make a jelly that acts as chain of oscillators with a fractal like resonance band. Hence, with the increasing detection resolution, in the vacant space between two energy levels of a given resonance band, a new band appears, due to fractal nature, generation of newer energy levels never stops. This is natural property of a linear chain oscillator. As we correlate each energy level of the resonance band of organic jelly, as a function of pH and density of the jelly, we realize a logic gate, whose truth table is finite, but if we zoom any small part, a new truth table appears. In principle, zooming of truth table would continue forever. Thus, we invent a new class of infinite logic gate for the first time.

Colbert Sesanker's insight:

 A practical realization of Anirban Bandyopadhyay's cosmology.  

"in the vacant space between two energy levels of a given resonance band, a new band appears, due to fractal nature, generation of newer energy levels never stops."

 

Reminds me of the Dedekind cut method of constructing real numbers. Don't be fooled. The appearance of a new frequency band depends on the 'detection resolution' which is finite. It's not infinite. 

 

Drawing frequency bands as you need them has the flavor of a functional programming style 'lazy evaluation' construct.

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Jack Tuszynski : Coherence in Biology Part I Winter 2015 (University of Alberta)

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Electrodynamic Signaling by the Dendritic Cytoskeleton (Google Workshop)

Google Workshop on Quantum Biology Electrodynamic Signaling by the Dendritic Cytoskeleton Presented by Jack Tuszynski October 22, 2010 ABSTRACT A model descr...
Colbert Sesanker's insight:

a bit old,  but one of the best overviews on the primary importance of the cytoskeleton

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Prof. RNDr. Jaroslav Flegr, CSc.: List of papers

Colbert Sesanker's insight:

Lots of papers on Toxoplasmosis and other markers that seem to influence behavior

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Evolutionary game theory: cells as players - (Molecular BioSystems)

Evolutionary game theory: cells as players -  (Molecular BioSystems) | Modern Biology | Scoop.it
In two papers we review game theory applications in biology below the level of cognitive living beings. It can be seen that evolution and natural selection replace the rationality of the actors appropriately. Even in these micro worlds, competing situations and cooperative relationships can be found and modeled by evolutionary game theory. Also those units of the lowest levels of life show different strategies for different environmental situations or different partners. We give a wide overview of evolutionary game theory applications to microscopic units. In this first review situations on the cellular level are tackled. In particular metabolic problems are discussed, such as ATP-producing pathways, secretion of public goods and cross-feeding. Further topics are cyclic competition among more than two partners, intra- and inter-cellular signalling, the struggle between pathogens and the immune system, and the interactions of cancer cells. Moreover, we introduce the theoretical basics to encourage scientists to investigate problems in cell biology and molecular biology by evolutionary game theory.
Colbert Sesanker's insight:

Clear and simple introduction to evolutionary game theory. Explains key ideas.

 

Explains:

 

*  Payoff Matrices

*  Nash Equilibria

*  Mixed Strategies

*  Evolutionary Stable Strategies

*  Enumerates all possible Two Player Game Strategies

*  Replicator Equation for dynamics of populations with

    different  strategies  

 

Did an interesting (3D cellular autonoma) workshop project on this, see:  https://sites.google.com/site/colbertsesankerresearch/outreach

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A theory of biological relativity: no privileged level of causation (The Royal Society, Denis Noble)

A theory of biological relativity: no privileged level of causation (The Royal Society,   Denis Noble) | Modern Biology | Scoop.it
Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of ‘biological relativity’ and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined.
Colbert Sesanker's insight:

Highlight:

" This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes.." 

 

Downward causation is an interesting concept. 

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