Complex Phenomena
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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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very new kind of science

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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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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.
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Earth Talk: Fritjof Capra - The Systems View of Life - YouTube

"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 he describes systemic thinking 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'. I think by 'machine' he means a linear "sum of parts" without any nonlinear dynamics between the parts?  Also implicitly assumes that systemic thinking is what allowed us to break off cartesian dualism and into panpsychism.   

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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


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Life as Evolving Software, Greg Chaitin at PPGC UFRGS - YouTube

"Few people remember Turing's work on pattern formation in biology (morphogenesis), but Turing's famous 1936 paper On Computable Numbers exerted an immense influence on the birth of molecular biology indirectly, through the work of John von Neumann on self-reproducing automata, which influenced Sydney Brenner who in turn influenced Francis Crick, the Crick of Watson and Crick, the discoverers of the molecular structure of DNA. Furthermore, von Neumann's application of Turing's ideas to biology is beautifully supported by recent work on evo-devo (evolutionary developmental biology). The crucial idea: DNA is multi-billion year old software, but we could not recognize it as such before Turing's 1936 paper, which according to von Neumann creates the idea of computer hardware and software."

 

Colbert Sesanker's insight:

the most interesting part is the relationship between innovation and incompleteness 

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Masao Ito

Masao Ito | Complex Phenomena | 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: http://www.amazon.com/The-Cerebellum-Brain-Implicit-Science/dp/0137050682/ref=sr_1_1?ie=UTF8&qid=1409703176&sr=8-1&keywords=cerebellum

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Subcortical Structures and Cognition - Implications for Neuropsychological Assessment

Subcortical Structures and Cognition - Implications for Neuropsychological Assessment | Complex Phenomena | Scoop.it

"The study of neuropsychology traditionally begins with geography: the neocortex as the seat of cognition and behavior, and the subcortical regions coordinating movement. Subcortical Structures and Cognition breaks with this traditional view, arguing for a practice-oriented rethinking of brain organization"

Colbert Sesanker's insight:

The sections on the cerebellum are very good

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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

int"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."

Colbert Sesanker's insight:

interesting but vague idea

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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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Colbert Sesanker's insight:

combine with integrated information

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A Neuroscientist's Radical Theory of How Networks Become Conscious | WIRED

A Neuroscientist's Radical Theory of How Networks Become Conscious | WIRED | Complex Phenomena | Scoop.it
It's a question that's perplexed philosophers for centuries and scientists for decades: Where does consciousness come from? Neuroscientist Christof Koch, chief scientific officer at the Allen Institute for Brain Science, thinks he has an answer.
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high level description of integrated information

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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.
Colbert Sesanker's insight:

"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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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:

i don't think the neurons are being pushed around as symbols. 

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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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Moths produce extremely quiet ultrasonic courtship songs by rubbing specialized scales

Moths produce extremely quiet ultrasonic courtship songs by rubbing specialized scales | Complex Phenomena | Scoop.it

"Our discovery of extremely low-intensity ultrasonic communication may point to a whole undiscovered world of private communication, using “quiet” ultrasound."


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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."

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Is there any unreasonable effectiveness of mathematics in biology? - Dominique Lambert - YouTube

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

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best people for unreasonable effectiveness arguments are Penrose and Tegmark

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How Information Theory Could Hold the Key to Quantifying Nature

How Information Theory Could Hold the Key to Quantifying Nature | Complex Phenomena | 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.


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

MaxEnt - physics meets ecology.

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

How Information Theory Could Hold the Key to Quantifying Nature

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Hector Zenil | Personal Homepage

Hector Zenil | Personal Homepage | Complex Phenomena | 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")."

 

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Note the people in the picture

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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... | Complex Phenomena | 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

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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."

Colbert Sesanker's insight:

subcortical processing of visual information? maybe not.

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Spectral Signatures of Reorganised Brain Networks in Disorders of Consciousness

Spectral Signatures of Reorganised Brain Networks in Disorders of Consciousness | Complex Phenomena | Scoop.it
What are the neural signatures of consciousness? This is an elusive yet fascinating challenge to current cognitive neuroscience, but it takes on an immediate clinical and societal significance in patients diagnosed as vegetative and minimally conscious. In these patients, it leads us to ask whether we can test for the presence of these signatures in the absence of any external signs of awareness. Recent conceptual advances suggest that consciousness requires a dynamic balance between integrated and differentiated networks of information exchange between brain regions. Here we apply this insight to study such networks in patients and compare them to healthy adults. Using the science of graph theory, we show that the rich and diversely connected networks that support awareness are characteristically impaired in patients, lacking the ability to efficiently integrate information across disparate regions via well-connected hubs. We find that the quality of patients' networks also correlates well with their degree of behavioural responsiveness, and some vegetative patients who show signs of hidden awareness have remarkably well-preserved networks similar to healthy adults.
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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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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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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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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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