Complex Phenomena
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Dancing Honeybee Using Vector Calculus to Communicate

honey bees describe flower location by dancing

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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 until, truly, all that's left is refined measurement and engineering.
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Your Brain Is On the Brink of Chaos - Issue 15: Turbulence - Nautilus

Your Brain Is On the Brink of Chaos - Issue 15: Turbulence - Nautilus | Complex Phenomena | Scoop.it

"At the same time, chaos has its advantages. On a behavioral level, the arms race between predator and prey has wired erratic strategies into our nervous system.1 A moth sensing an echolocating bat, for example, immediately directs itself away from the ultrasound source. The neurons controlling its flight fire in an increasingly erratic manner as the bat draws closer, until the moth, darting in fits, appears to be nothing but a tumble of wings and legs. More generally, chaos could grant our brains a great deal of computational power, by exploring many possibilities at great speed."

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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."

Colbert Sesanker's insight:

see the talk: https://www.solveforx.com/moonshots/the-fourth-phase-of-water-dr-gerald-pollack-at-tedxguelphu

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Epigenetics: The sins of the father

Epigenetics: The sins of the father | Complex Phenomena | Scoop.it

"The roots of inheritance may extend beyond the genome, but the mechanisms remain a puzzle

 

Dias had been exposing male mice to acetophenone — a chemical with a sweet, almond-like smell — and then giving them a mild foot shock. After being exposed to this treatment five times a day for three days, the mice became reliably fearful, freezing in the presence of acetophenone even when they received no shock.

 

Ten days later, Dias allowed the mice to mate with unexposed females. When their young grew up, many of the animals were more sensitive to acetophenone than to other odours, and more likely to be startled by an unexpected noise during exposure to the smell. Their offspring — the 'grandchildren' of the mice trained to fear the smell — were also jumpier in the presence of acetophenone. What's more, all three generations had larger-than-normal 'M71 glomeruli', structures where acetophenone-sensitive neurons in the nose connect with neurons in the olfactory bulb. In the January issue of Nature Neuroscience1, Dias and Ressler suggested that this hereditary transmission of environmental information was the result of epigenetics — chemical changes to the genome that affect how DNA is packaged and expressed without altering its sequence."

Colbert Sesanker's insight:

How does it get to the germ line?

 

"The first question is how the effects of environmental exposure become embedded in an animal's germ cells — in this case, the mouse's sperm. Germ cells have been shown to express olfactory receptors11. So it is possible that Olfr151 receptors in sperm respond to odorant molecules in the bloodstream and then change the methylation of the corresponding gene in sperm DNA.

 

Alternatively, after being exposed to the odour and the pain, a mouse might produce RNA molecules — perhaps in the brain — that make their way into the bloodstream and then selectively target the Olfr151 gene in sperm. Many studies in plants have hinted at this sort of systemic RNA shuttling. RNA molecules expressed in a plant's leaf, for example, can travel through its vascular system to many of its other tissues and affect gene expression12."

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Can a Single Neuron Tell Halle Berry From Grandma Esther? | DiscoverMagazine.com

Can a Single Neuron Tell Halle Berry From Grandma Esther? | DiscoverMagazine.com | Complex Phenomena | Scoop.it

"Four decades ago, an MIT neuroscientist named Jerry Lettvin had a sudden inspiration about how our brains make sense of the world. What if each of us had a special set of neurons in our head whose only job was to recognize a particular person, place, or thing? It was a strange idea, but given what Lettvin knew about the brain, it was plausible. "

Colbert Sesanker's insight:

sparse coding networks? now that sounds like...

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The Behavioral Ecology of Insect Vibrational Communication

The Behavioral Ecology of Insect Vibrational Communication | Complex Phenomena | Scoop.it

"Vibrational communication is widespread in insect social and ecological interactions. Of the insect species that communicate using sound, water surface ripples, or substrate vibrations, we estimate that 92% use substrate vibrations alone or with other forms of mechanical signaling. Vibrational signals differ dramatically from airborne insect sounds, often having low frequencies, pure tones, and combinations of contrasting acoustic elements. Plants are the most widely used substrate for transmitting vibrational signals. Plant species can vary in their signal transmission properties, and thus host plant use may influence signal divergence. Vibrational communication occurs in a complex environment containing noise from wind and rain, the signals of multiple individuals and species, and vibration-sensitive predators and parasitoids. We anticipate that many new examples and functions of vibrational communication will be discovered, and that study of this modality will continue to provide important insights into insect social behavior, ecology, and evolution."

Colbert Sesanker's insight:

interestingly plants serve as mediums for communication between insects. a kind of telephone

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Wow! Moths Jam Bat Sonar

Wow! Moths Jam Bat Sonar | Complex Phenomena | Scoop.it

"Tiger moths can thwart attacks from bats by effectively jamming the bats' sonar, doing so by emitting sudden bursts of ultrasound, scientists now find.

Past research had revealed that many night-flying moths have evolved the ability to hear bat sonar. A number were even seen responding with clicks of ultrasound.

Other studies revealed that moth ultrasound could startle bats off. Research also showed the outbursts could warn bats that such moths had a nasty taste, just as flashy colors on some animals can serve to ward off potential predators. Still, there was the enticing possibility that some moths used ultrasound to actually foil bat sonar."

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Underground allies: how and why do mycelial networks help plants... - PubMed - NCBI

"Most land plants associate with mycorrhizal fungi that can connect roots of neighboring plants in common mycelial networks (CMNs). Recent evidence shows that CMNs transfer warning signals of pathogen and aphid attack between plants. However, we do not know how defence-related signaling via CMNs operates or how ubiquitous it is. Nor do we know what the ecological relevance and fitness consequences are, particularly from the perspective of the mycorrhizal fungus. Here, we focus on the potential fitness benefits for mycorrhizal fungi and outline hypothetical scenarios in which signal transfer via CMNs is modulated in order to acquire the most benefit for the fungus (i.e. acquisition of carbon) for minimal cost. We speculate that the signal may be quantitative and may elicit plant defence responses on different levels depending on the distance the signal is transferred. Finally, we discuss the possibility of practical applications of this phenomenon for crop protection."

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Electrical signals and their physiological significance in plants - FROMM - 2006 - Plant, Cell & Environment - Wiley Online Library

Electrical signals and their physiological significance in plants - FROMM - 2006 - Plant, Cell & Environment - Wiley Online Library | Complex Phenomena | Scoop.it

"Electrical excitability and signalling, frequently associated with rapid responses to environmental stimuli, are well known in some algae and higher plants. The presence of electrical signals, such as action potentials (AP), in both animal and plant cells suggested that plant cells, too, make use of ion channels to transmit information over long distances. In the light of rapid progress in plant biology during the past decade, the assumption that electrical signals do not only trigger rapid leaf movements in ‘sensitive’ plants such as Mimosa pudica orDionaea muscipula, but also physiological processes in ordinary plants proved to be correct. Summarizing recent progress in the field of electrical signalling in plants, the present review will focus on the generation and propagation of various electrical signals, their ways of transmission within the plant body and various physiological effects."

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How Plants Secretly Talk to Each Other | Science | WIRED

How Plants Secretly Talk to Each Other | Science | WIRED | Complex Phenomena | Scoop.it

"It’s now well established that when bugs chew leaves, plants respond by releasing volatile organic compounds into the air. By Karban’s last count, 40 out of 48 studies of plant communication confirm that other plants detect these airborne signals and ramp up their production of chemical weapons or other defense mechanisms in response. “The evidence that plants release volatiles when damaged by herbivores is as sure as something in science can be,” said Martin Heil, an ecologist at the Mexican research institute Cinvestav Irapuato. “The evidence that plants can somehow perceive these volatiles and respond with a defense response is also very good.”

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Tyler Lab

Tyler Lab | Complex Phenomena | Scoop.it
Tyler Laboratory of Neuroscience and Neurotechnology at the Virginia Tech Carilion Research Institute and the School of Biomedical Engineering and Sciences at Virginia Tech. We study the influence of mechanical forces on brain activity, develop tools and approaches to mapping functional brain activity in humans using ultrasound, and engineer neurotechnology for nonivasively stimulating brain activity using ultrasound, tDCS, and TMS while monitoring activity in human brain circuits using EEG, fMRI, and fNIRS.
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Neurons are responsive to ultrasound 

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One of the strangest animals on earth gets a little weirder

One of the strangest animals on earth gets a little weirder | Complex Phenomena | Scoop.it

"Mantis shrimp, the psychedelic reef-dwellers that can wallop their prey with an astounding 200 pounds of force, have a large collection of unique qualities. One is an unusually large number of photoreceptors, the light-sensing proteins that contribute to color vision. Humans have three types of color receptors, birds and reptiles have four, and mantis shrimp have an astounding 12 different kinds."

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At the gene level, robustness and evolvability go hand in hand

At the gene level, robustness and evolvability go hand in hand | Complex Phenomena | Scoop.it

Robustness, the maintenance of a character in the presence of genetic change, can help preserve adaptive traits but also may hinder evolvability, the ability to bring forth novel adaptations. We used genotype networks to analyze the binding site repertoires of 193 transcription factors from mice and yeast, providing empirical evidence that robustness and evolvability need not be conflicting properties. Network vertices represent binding sites where two sites are connected if they differ in a single nucleotide. We show that the binding sites of larger genotype networks are not only more robust, but the sequences adjacent to such networks can also bind more transcription factors, thus demonstrating that robustness can facilitate evolvability.


Via Ashish Umre
Colbert Sesanker's insight:

Andreas Wagner's  new paper

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Evidence for complex, collective dynamics and emergent, distributed computation in plants

"It has been suggested that some biological processes are equivalent to computation, but quantitative evidence for that view is weak. Plants must solve the problem of adjusting stomatal apertures to allow sufficient CO2 uptake for photosynthesis while preventing excessive water loss. Under some conditions, stomatal apertures become synchronized into patches that exhibit richly complicated dynamics, similar to behaviors found in cellular automata that perform computational tasks. Using sequences of chlorophyll fluorescence images from leaves of Xanthium strumarium L. (cocklebur), we quantified spatial and temporal correlations in stomatal dynamics. Our values are statistically indistinguishable from those of the same correlations found in the dynamics of automata that compute. These results are consistent with the proposition that a plant solves its optimal gas exchange problem through an emergent, distributed computation performed by its leaves."

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Transfer Entropy and Transient Limits of Computation

Transfer entropy is a recently introduced information-theoretic measure quantifying directed statistical coherence between spatiotemporal processes, and is widely used in diverse fields ranging from finance to neuroscience. However, its relationships to fundamental limits of computation, such as Landauer's limit, remain unknown. Here we show that in order to increase transfer entropy (predictability) by one bit, heat flow must match or exceed Landauer's limit. Importantly, we generalise Landauer's limit to bi-directional information dynamics for non-equilibrium processes, revealing that the limit applies to prediction, in addition to retrodiction (information erasure). Furthermore, the results are related to negentropy, and to Bremermann's limit and the Bekenstein bound, producing, perhaps surprisingly, lower bounds on the computational deceleration and information loss incurred during an increase in predictability about the process. The identified relationships set new computational limits in terms of fundamental physical quantities, and establish transfer entropy as a central measure connecting information theory, thermodynamics and theory of computation.

 

Transfer Entropy and Transient Limits of Computation
Mikhail Prokopenko and Joseph T. Lizier
Scientific Reports 4, 5394, doi:10.1038/srep05394
http://www.nature.com/srep/2014/140623/srep05394/full/srep05394.html


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From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0

From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0 | Complex Phenomena | Scoop.it

This paper presents Integrated Information Theory (IIT) of consciousness 3.0, which incorporates several advances over previous formulations. IIT starts from phenomenological axioms: information says that each experience is specific – it is what it is by how it differs from alternative experiences; integration says that it is unified – irreducible to non-interdependent components; exclusion says that it has unique borders and a particular spatio-temporal grain. These axioms are formalized into postulates that prescribe how physical mechanisms, such as neurons or logic gates, must be configured to generate experience (phenomenology). The postulates are used to define intrinsic information as “differences that make a difference” within a system, and integrated information as information specified by a whole that cannot be reduced to that specified by its parts. By applying the postulates both at the level of individual mechanisms and at the level of systems of mechanisms, IIT arrives at an identity: an experience is a maximally irreducible conceptual structure (MICS, a constellation of concepts in qualia space), and the set of elements that generates it constitutes a complex. According to IIT, a MICS specifies the quality of an experience and integrated information ΦMax its quantity. From the theory follow several results, including: a system of mechanisms may condense into a major complex and non-overlapping minor complexes; the concepts that specify the quality of an experience are always about the complex itself and relate only indirectly to the external environment; anatomical connectivity influences complexes and associated MICS; a complex can generate a MICS even if its elements are inactive; simple systems can be minimally conscious; complicated systems can be unconscious; there can be true “zombies” – unconscious feed-forward systems that are functionally equivalent to conscious complexes.

 


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Sperm RNA carries marks of trauma

Sperm RNA carries marks of trauma | Complex Phenomena | Scoop.it
Stress alters the expression of small RNAs in male mice and leads to depressive behaviours in later generations.
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"When raised this way, male offspring showed depressive behaviors and tended to underestimate risk, the study found. Their sperm also showed abnormally high expression of five microRNAs. One of these, miR-375, has been linked to stress and regulation of metabolism."

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12 Real Parasites That Control the Lives of Their Hosts

12 Real Parasites That Control the Lives of Their Hosts | Complex Phenomena | Scoop.it
Many parasites are satisfied with just living off of their hosts, while others decide their hosts must die. But there are also some parasites who can change their hosts' behavior or physiology in ways fit only for science fiction. Here are 12 parasites who manipulate their hosts in incredible ways.
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Sound Garden: Can Plants Actually Talk and Hear?

Sound Garden: Can Plants Actually Talk and Hear? | Complex Phenomena | Scoop.it

"And there is evidence that insects and plants "hear" each other's sounds. Bees buzz at just the right frequency to release pollen from tomatoes and other flowering plants. And bark beetles may pick up the air bubble pops inside a plant, a hint that trees are experiencing drought stress."

Colbert Sesanker's insight:

good summary of plant acoustic signaling

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"Vibrational communication in insects and spiders" : Map of Life

Numerous animals use vibrations propagating through a substrate to communicate with conspecifics, predators or prey. This mode of communication has reached extraordinary heights in insects and spiders, where it is both highly sophisticated and remarkably diverse in function. Vibrational signals are probably not very costly to produce for such small animals, whereas the effective generation of air-borne sound is constrained by body size. However, the vibrations created by insects and spiders do not range further than a few metres, but relative to the size of these arthropods this is actually quite substantial. Until recently, vibrational communication had received very little attention, but now a growing number of studies is revealing more and more examples and roles of vibrational signals.'
Colbert Sesanker's insight:

portias can mask their presence on another spiders web by imitating current wind patterns in real time. They can also fake vibrational patterns of struggling insects. The difference between a struggling insect, wind/noise and a predator is quite subtle. This is some pretty insane signal processing. 

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Plant Talk | The Scientist Magazine®

Plant Talk | The Scientist Magazine® | Complex Phenomena | Scoop.it
Plants communicate and interact with each other, both aboveground and below, in surprisingly subtle and sophisticated ways.
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this one includes underground root networks of communication

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BMC Ecology | Full text | Love thy neighbour: facilitation through an alternative signalling modality in plants

Both competitive and facilitative interactions between species play a fundamental role in shaping natural communities. A recent study showed that competitive interactions between plants can be mediated by some alternative signalling channel, extending beyond those channels studied so far (i.e. chemicals, contact and light). Here, we tested whether such alternative pathway also enables facilitative interactions between neighbouring plant species. Specifically, we examined whether the presence of a ‘good’ neighbouring plant like basil positively influenced the germination of chilli seeds when all known signals were blocked. For this purpose, we used a custom-designed experimental set-up that prevented above- and below-ground contact and blocked chemical and light-mediated signals normally exchange by plants.
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Frontiers | How plausible is a subcortical account of rapid visual recognition? | Frontiers in Human Neuroscience

"Primates recognize objects in natural visual scenes with great rapidity. The ventral visual cortex is usually assumed to play a major role in this ability (“high-road”). However, the “low-road” alternative frequently proposed is that the visual cortex is bypassed by a rapid subcortical route to the amygdala, especially in the case of biologically relevant and emotional stimuli. This paper highlights the lack of evidence from psychophysics and computational models to support this “low-road” alternative. Most importantly, the timing of neural responses invites a serious reconsideration of the low-road role in rapid processing of visual objects."

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subcortical processing of visual information? maybe not.

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Quantum Biology: Better Living Through Quantum Mechanics - The Nature of Reality

Quantum Biology: Better Living Through Quantum Mechanics - The Nature of Reality | Complex Phenomena | Scoop.it

Seth Loyd: "A quantum computer is a serious piece of hardware. My colleagues and I build quantum computers from superconducting systems, quantum dots, lasers operating on nonlinear crystals..."


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Nice review of quantum effects in biology by seth loyd

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SEEING AND COMMUNICATING THROUGH WEAK ELECTRIC FIELDS

SEEING AND COMMUNICATING THROUGH WEAK ELECTRIC FIELDS | Complex Phenomena | Scoop.it

"Bruce Carlson and his colleagues from Washington University in St Louis, USA, explain that electric fish not only convey information about themselves in the structure of each electric pulse but also vary the duration of the interval between pulses to communicate their behavioural state, such as whether they are subordinate or dominant and how aggressive they are (p. 2365). All sensory information is encoded by neurons into patterns of electrical spikes. In the case of electric signal perception by mormyrids, information is encoded by specialised receptors known as knollenorgans into both spike timing differences between receptors and interspike intervals within receptors. Carlson and his colleagues also describe how two subfamilies of pulse-type African mormyrids differ in their ability to distinguish differences in the waveform of emitted electric signals and they explain that these perceptual differences are due to differences in midbrain structures, as well as differences in the distribution of the knollenorgan receptors on the fish's bodies. The authors conclude by saying, ‘The mormyrid electric communication pathway is a powerful model for integrating mechanistic studies of temporal coding with evolutionary studies of correlated differences in brain and behaviour to investigate neural mechanisms for processing temporal codes.’"

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Biophoton Communication: Can Cells Talk Using Light? | MIT Technology Review

Biophoton Communication: Can Cells Talk Using Light? | MIT Technology Review | Complex Phenomena | Scoop.it
A growing body of evidence suggests that the molecular machinery of life emits and absorb photons. Now one biologist has evidence that this light is a new form of cellular communication.
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