Modern Biology
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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 - Artificial Intelligence & The Future Of Civilization

Stephen Wolfram is a distinguished scientist, inventor, author, and business leader, is Founder & CEO, Wolfram Research; Creator, Mathematica, Wolfram|Alph
Colbert Sesanker's insight:
Wolfram 'gets it'. How courageous to spend his life fighting for the truth .. 
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The Calculi of Emergence: Computation, Dynamics and Induction

An observer's notion of what is ordered, what is random, and what is complex in its environment depends directly on its computational resources: the amount of raw measurement data, of memory, and of time available for estimation and inference. 
 

This paper presents an overview of an inductive framework-hierarchical ϵ-machine reconstruction—in which the emergence of complexity is associated with the innovation of new computational model classes. Complexity metrics for detecting structure and quantifying emergence, along with an analysis of the constraints on the dynamics of innovation, are outlined. Illustrative examples are drawn from the onset of unpredictability in nonlinear systems, finitary nondeterministic processes, and cellular automata pattern recognition. They demonstrate how finite inference resources drive the innovation of new structures and so lead to the emergence of complexity.

Colbert Sesanker's insight:

Crutchfield, James P. "The Calculi of Emergence: Computation, Dynamics and Induction." Physica D: Nonlinear Phenomena 75.1 (1994): 11-54.

Algorithmic Information Theory style formalization of Emergence,  Top down causation. and Complexity. 

 

Abstracts an observer, O, and defines the complexity measures relative to O.

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Hector Zenil (Oxford) publications

Hector Zenil (Oxford) publications | Modern Biology | Scoop.it

"My research focuses on applying information theory and complexity science to genomics, synthetic and network biology. With backgrounds in math, computer science and philosophy, I think of myself as a kind ofexperimental philosopher or a computational natural scientist. (Greg Chaitin once referred to me as a "new kind of practical theoretician")."

 

Colbert Sesanker's insight:

Contributions to the aesthetically justified  dream of unlocking the binary code of nature

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Proceedings of the royal Society (2013): The evolutionary origins of modularity

Proceedings of the Royal Society, Jan 2013:

 

"Experiments with selection pressures to maximize network perfor-
mance and minimize connection costs yield networks that
are significantly more modular and more evolvable than con-
trol experiments that only select for performance."

 

Colbert Sesanker's insight:

This paper demonstrates the emergence of modularity in networks artificially evolved to maximize performance and minimize connection cost. Compare with previous attempts that argue modularity is under selective pressure to convey evolvability. 

 

 

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Zuse's Thesis - Zuse hypothesis - Algorithmic Theory of Everything - Digital Physics, Rechnender Raum (Computing Space, Computing Cosmos) - Computable Universe - The Universe is a Computer - Theory...

Zuse's Thesis - Zuse hypothesis - Algorithmic Theory of Everything - Digital Physics, Rechnender Raum (Computing Space, Computing Cosmos) - Computable Universe - The Universe is a Computer - Theory... | Modern Biology | Scoop.it

"Konrad Zuse (1910-1995; pronounce: "Conrud Tsoosay") not only built the first programmable computers (1935-1941) and devised the first higher-level programming language (1945), but also was the first to suggest (in 1967) that the entire universe is being computed on a computer, possibly a cellular automaton (CA). He referred to this as "Rechnender Raum" or Computing Space or Computing Cosmos. Many years later similar ideas were also published / popularized / extended by Edward Fredkin (1980s), Jürgen Schmidhuber (1990s - see overview), and more recently Stephen Wolfram (2002) (see comments and Edwin Clark's review page ). Zuse's first paper on digital physics and CA-based universes was:

 

Konrad Zuse, Rechnender Raum, Elektronische Datenverarbeitung, vol. 8, pages 336-344, 1967.

 

Zuse is careful: on page 337 he writes that at the moment we do not have full digital models of physics, but that does not prevent him from asking right there: which would be the consequences of a total discretization of all natural laws? For lack of a complete automata-theoretic description of the universe he continues by studying several simplified models. He discusses neighbouring cells that update their values based on surrounding cells, implementing the spread and creation and annihilation of elementary particles. On page 341 he writes "In all these cases we are dealing with automata types known by the name "cellular automata" in the literature" and cites von Neumann's 1966 book: Theory of self-reproducing automata. On page 342 he briefly discusses the compatibility of relativity theory and CAs."

 

Colbert Sesanker's insight:

There is a lot of babble on this now. See: https://www.youtube.com/watch?v=PKkiy24LqBQ

 

Thinking back to some of Tesla's words:

 "To me, the universe is simply a great machine which never came into being and never will end. The human being is no exception to the natural order. Man, like the universe, is a machine. Nothing enters our minds or determines our actions which is not directly or indirectly a response to stimuli beating upon our sense organs from without."

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Protein Science: 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:

In particular: 

" 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." 
 
"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). "
 

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Physical Review Letters: Could Humans Recognize Odor by Phonon Assisted Tunneling?

Physical Review Letters: Could Humans Recognize Odor by Phonon Assisted Tunneling? | Modern Biology | 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

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Nature News: Flies sniff out heavy hydrogen

Nature News: Flies sniff out heavy hydrogen | Modern Biology | 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:

see luca turin's vibration theory of smell

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Current Opinion in Structural Biology: Electrostatic aspects of protein–protein interactions

Structural and mutational analyses reveal a central role for electrostatic interactions in protein–protein association. Experiment and theory both demonstrate that clusters of charged and polar residues that are located on protein–protein interfaces may enhance complex stability, although the total effect of electrostatics is generally net destabilizing. The past year also witnessed significant progress in our understanding of the effect of electrostatics on protein association kinetics, specifically in the characterization of a partially desolvated encounter complex.
Colbert Sesanker's insight:

The induced fit model considers local protein deformations and local electrostatic interactions but denies long range coulomb interactions generated by an excited protein.

 

Update: These long range electrostatic interactions and their role in enzyme kinetics have recently been verified.  

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Science: Probing Allostery Through DNA

Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which—together with molecular dynamics simulations—suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.
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Is there any unreasonable effectiveness of mathematics in biology? - Dominique Lambert

basonAn open lecture of Professor Dominique Lambert (University of Namur, Belgium), a renowned expert in the field of theoretical physics and philosophy of scienc...

Colbert Sesanker's insight:

best people for unreasonable effectiveness arguments are Penrose and Tegmark. One caution is that the mathematics described here is being fit to really high level properties like observed 'shapes' and 'patterns' 

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QBism puts the scientist back into science (Nature)

QBism puts the scientist back into science (Nature) | Modern Biology | Scoop.it
Schrödinger wrote in a little-known 1931 letter2 to German physicist Arnold Sommerfeld that quantum mechanics “deals only with the object–subject relation”. Another founder of quantum mechanics, Danish physicist Niels Bohr, insisted in a 1929 essay3 that the purpose of science was not to reveal “the real essence of the phenomena” but only to find “relations between the manifold aspects of our experience”
Colbert Sesanker's insight:

the moral interpretation 

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The Case Against Reality

The Case Against Reality | Modern Biology | Scoop.it
A professor of cognitive science argues that the world is nothing like the one we experience through our senses.
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Non-dual mathematical theory of Reality.
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An Information-Theoretic Formalism for Multiscale Structure in Complex Systems

We develop a general formalism for representing and understanding structure in complex systems. In our view, structure is the totality of relationships among a system's components, and these relationships can be quantified using information theory. In the interest of flexibility we allow information to be quantified using any function, including Shannon entropy and Kolmogorov complexity, that satisfies certain fundamental axioms. Using these axioms, we formalize the notion of a dependency among components, and show how a system's structure is revealed in the amount of information assigned to each dependency. We explore quantitative indices that summarize system structure, providing a new formal basis for the complexity profile and introducing a new index, the "marginal utility of information". Using simple examples, we show how these indices capture intuitive ideas about structure in a quantitative way. Our formalism also sheds light on a longstanding mystery: that the mutual information of three or more variables can be negative. We discuss applications to complex networks, gene regulation, the kinetic theory of fluids and multiscale cybernetic thermodynamics.

 

An Information-Theoretic Formalism for Multiscale Structure in Complex Systems
Benjamin Allen, Blake C. Stacey, Yaneer Bar-Yam

http://arxiv.org/abs/1409.4708


Via Complexity Digest
Colbert Sesanker's insight:

Very clearly written and worth reading. Not just another paper on information and complexity.  Provides a  definition of a complex system.

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Intelligence and the Computational Universe

Colbert Sesanker's insight:

One of the best talks. I think it's really cool that's he's actually using some of the NKS simple program search ideas in wolfram alpha's natural language component. 

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John Harte (Berkley): How Information Theory Could Hold the Key to Quantifying Nature

John Harte (Berkley): How Information Theory Could Hold the Key to Quantifying Nature | Modern Biology | Scoop.it

The Western Ghats in India rise like a wall between the Arabian Sea and the heart of the subcontinent to the east. The 1,000-mile-long chain of coastal mountains is dense with lush rainforest and grasslands, and each year, clouds bearing monsoon rains blow in from the southwest and break against the mountains’ flanks, unloading water that helps make them hospitable to numerous spectacular and endangered species. The Western Ghats are one of the most biodiverse places on the planet. They were also the first testing ground of an unusual new theory in ecology that applies insights from physics to the study of the environment.


Via Ashish Umre
Colbert Sesanker's insight:

At some point we will have everything in binary and it will be beautiful. 

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Gary Bamford's curator insight, September 27, 2014 3:04 AM

MaxEnt - physics meets ecology.

Nevermore Sithole's curator insight, October 7, 2014 4:26 AM

How Information Theory Could Hold the Key to Quantifying Nature

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Stephen Wolfram: 'Can We Really Be the Smartest Things in the Universe? | Inc. Magazine

Physicist Stephen Wolfram, who invented Mathematica software and the Wolfram Alpha search engine, explains how intelligent behavior is really just sophisticated computation--and how that's the underpinning of his inventions.
Colbert Sesanker's insight:

See 45:00 in the above "Intelligence and The Computational Universe "Talk

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Nature: Gut–brain link grabs neuroscientists

Nature: Gut–brain link grabs neuroscientists | Modern Biology | 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.

 

See Rob Kinght's TED talk below which supports the idea for the microbiome's role in cognition.

 

 

 

 

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

Cell: Effects of the gut microbiota on bone mass: Trends in Endocrinology & Metabolism | Modern Biology | 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.

 

Colbert Sesanker's insight:

Microbiome immune system interactions are fascinating. 

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How our microbes make us who we are (TED, Rob Knight)

How our microbes make us who we are (TED, Rob Knight) | Modern Biology | Scoop.it
Rob Knight is a pioneer in studying human microbes, the community of tiny single-cell organisms living inside our bodies that have a huge — and largely unexplored — role in our health. “The three pounds of microbes that you carry around with you might be more important than every single gene you carry around in your genome,” he says. Find out why.
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Luca Turin (MIT): A Quantum of Solace - Molecular Electronics of Benzodiazepines

"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.  

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Oxford Journals (PEDS): 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:

May be related to coherent excitations idea as these can excite proteins and increase their affinities towards their substrates 

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Earth Talk: Fritjof Capra - The Systems View of Life

"A talk given at Schumacher College (UK), Dartington on May 7th 2014.

The great challenge of our time is to build and nurture sustainable communities, designed in such a manner that their ways of life, physical structures, and technologies do not interfere with nature's inherent ability to sustain life. To do so, requires a new ecological understanding of life, as well as a new kind of "systemic" thinking.

In this lecture, Fritjof Capra describes that such a new understanding of life in terms of complexity, networks, and patterns of organization, has recently emerged at the forefront of science. He will emphasize, in particular, the new conception of the nature of mind and consciousness, which is one of the most radical philosophical implications of the systemic understanding of life; and the urgency of this new understanding for dealing with our global ecological crisis and protecting the continuation and flourishing of life on Earth.

Fritjof Capra was speaking as part of his short course running at Schumacher College."

Colbert Sesanker's insight:

In the book systemic thinking is described as if it is  non-mechanistic and somehow makes room for qualia, social and political issues. There is nothing presented to suggest living organisms are more than 'machines'.  Also implicitly assumes that systemic thinking is what allowed us to break off Cartesian dualism and into panpsychism. 

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Bayesian Interpretation of Quantum Mechanics (Christopher A. Fuchs)

Bayesian Interpretation of Quantum Mechanics (Christopher A. Fuchs) | Modern Biology | Scoop.it

"The world we live in is well-described by quantum mechanics. What should we make of that? In a way, the answer to this question was once less positive than it is today. For although quantum theory is a tool of unprecedented accuracy in predicting and controlling the phenomena about us---and by way of that is the basis of our technological society---the intellectual lesson we have come to derive from it has been one largely of limitations. The best place to see this attitude at work is in a standard presentation of the Heisenberg uncertainty relations. It is almost as if the world were holding something back that we really had every right to possess: the task of physics, or so it was believed, is simply to sober up to this fact and make the best of it.

 

In contrast to this textbook lesson, the last five years have seen the start of a significantly more positive, almost intoxicating, attitude about the basic role of quantum mechanics. This is evidenced no more clearly than within the small, but growing, community of workers in Quantum Information Theory and Quantum Computing. The point of departure in both these disciplines is not to ask what limits quantum mechanics places upon us, but instead what novel, productive things we can do in the quantum world that we could not have done otherwise. In what ways can we say that the quantum world is fantastically better than the classical world?"

Colbert Sesanker's insight:

"QBism would say, it’s not that the world is built up from stuff on “the outside” as the Greeks would have had it. Nor is it built up from stuff on “the inside” as the idealists, like George Berkeley and Eddington, would have it. Rather, the stuff of the world is in the character of what each of us encounters every living moment — stuff that is neither inside nor outside, but prior to the very notion of a cut between the two at all."

 

sounds very non-dual and idealistic.. 

 

from the quanta magazine article: https://www.quantamagazine.org/20150604-quantum-bayesianism-qbism/

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Masao Ito (RIKEN Brain Science Institute)

Masao Ito (RIKEN Brain Science Institute) | Modern Biology | Scoop.it

"Masao Ito is Special Advisor to the RIKEN Brain Science Institute, Japan.  He received the Fujiwara Prize (1981), the Academy Prize and Imperial Prize (1986), the Robert Dow Neuroscience Award (1993), the IPSEN Foundation Award (1993), the Person of Cultural Merit (1994), the Japan Prize (1996), Order of Culture (1996), and an Honorary Degree of Science from The University of Southern California (1995) and from Torino University (1996).  Dr. Ito's field is neuroscience. He discovered the inhibitory action of cerebellar Purkinje cells, and the characteristic synaptic plasticity, long-term depression (LTD), in these cells. Based upon these findings, he developed a theory that the cerebellum is a general learning machine for acquiring not only motor skills, but also implicit memory in thought."

 

Colbert Sesanker's insight:

Do some research on Ito's views on the cerebellum's role in cognition. Too interesting to spell out here.

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