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Mark Bruce
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SciTech #ScienceSunday Digest - 39/2016.
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Fixing DNA damage, Modular synbio pellets, Towards head transplant, Custom acoustic holograms, Advanced drone systems, Wireless emotion detection, Atomically precise molecular syntheses, Metastasis gene therapy, Wireless MEMS, Sewing robot.

1. Compensating for DNA Damage
New work by the SENS Research Foundation has successfully achieved stable allotropic expression (in the nucleus), import (into mitochondria), and assembly into functional protein complexes able to rescue the cell and metabolism from mutations in the mitochondrial copies of these genes With some additional work and tricks the group hope the demonstration will allow all 13 mitochondrial genes to be moved to the nucleus and so solve one of the seven causes of aging damage, which will be important for things like sarcopenia In related work human cells engineered to contain a copy of the Dsup gene from tardigrades suffered 50% fewer DNA mutations as a result of prolonged exposure to X-rays; the group hope to discover related protective genes that grant tardigrades their resilience and the possibility is open to gene therapies to reduce DNA mutation rates in humans.

2. Modular DNA Expression Pellets
You can now produce bulk freeze-dried pellets containing the key cellular components needed for translating DNA to proteins - all of the enzymes, ribosomes, tRNA, etc that you need to do this basic protein production process The idea is that you’d have a supply of these pellets (room temp shelf-life > 1 year) and when you needed to conduct a test or produce a protein you’d synthesise your gene or DNA of interest and add it to a pellet in some water. Such cell-free synthesis is an exciting technology, another tiny step towards atomically-precise synthesis, and something that would be immediately useful for remote or at-home applications above and beyond those demonstrated: protein vaccines, antimicrobial peptides, multi-enzyme production for metabolic pathway to create a complex organic drug molecule, antibodies for diagnostics, etc.

3. Towards Human Head Transplant
Recent previous work in mice and recent work in dogs a modified solution of polyethylene glycol has been used to at least partially restore the neural connections in animals whose spines have been almost completely severed In the recent dog experiment the dog apparently regained the ability to walk after about three weeks. Surgeon Sergio Canavero plans to use these result to press forward with the first ever human head transplant next year, using the technique to help reconnect the severed spine of the patient’s head with the donor body. Others demand that at the lack of detailed histology data of the supposedly repaired spinal interface damages the case for proceeding in humans.

4. Custom Acoustic Holograms
Three dimensional acoustic holograms take a big step forward with a new system that uses a single powerful ultrasound transducer onto which is placed a 3D printed block that has been precisely patterned to form an acoustic hologram; ultrasound passing through the block is forced into the desired custom waveform, to levitate objects for example Such a device produces an acoustic hologram with a resolution 100 times greater than previously possible with separate transducer systems. While working in air or water it can’t produce a dynamically changing waveform to move objects, although movement along fixed paths is possible. One possible way around this is to encode multiple sound fields at different frequencies to add some dynamic options.

5. Delivery, Security, Navy, Surveillance Drones
First, a cool new long range delivery drone combines a biplane design with VTOL and fixed-wing capabilities to get the best of both worlds Second, Aptonomy is launching a large security drone to monitor protected areas and intercept tresspassers Third, the Navy’s Blackwing drone platform is designed to be launched by submarine to provide wide-area surveillance and control of other drone and communications assets Finally, DARPA’s Aerial Dragnet system is being designed to provide persistent wide-area surveillance of areas such as cities via networked drone swarms

6. Detecting Emotions with Wireless Signals
EQ-Radio is a system that uses wireless signals and reflections to measure subtle changes in a person’s breathing and heart rhythms in order to determine their emotional state In recent tests the system was able to correctly predict whether the person was excited, happy, angry, or sad 87% of the time. Capturing human emotional states in such a way, particularly when not visibly obvious, would have uses in a wide range of different areas including security monitoring crowded events, entertainment, health care, consumer preferences, etc. The system measures heartbeats as accurately as an ECG monitor with an error margin of 0.3%.

7. Atomically Precise Molecular Chains
The size of alternative atomically precise materials that can be synthesised keeps getting larger with this recent creation of atomically precise gold nanoparticles enshrouded with a functional molecular shell and linked via a precise molecular bridge Progressively building up such units would allow the creation of ever-larger precise crystalline materials with novel electrochemical properties given that the electron clouds of the metal cores become coupled. There are also efforts to build more sophisticated catalysts by precisely combining palladium with ruthenium in different mixed or shelled structures

8. Gene Therapy Stops Cancer Metastasis
A gene therapy technique involving the delivery of microRNAs of a specific sequence into cancer cells is successful in preventing those cancer cells from undergoing metastatic spread through the body These microRNAs specifically regulate and block the expression of the Palladin protein that helps drive metastasis, and was delivered in this case from microRNAs embedded in nanoparticles that were loaded into a hydrogel scaffold that was subsequently implanted into the mice. Such a tool is a viable approach to cancer treatment in combination with other cancer-killing approaches. In related gene editing news, Synthego launches a CRISPR kit for labs and DIYers to make CRISPR editing easier

9. Wireless MEMS
A microelectromechanical device has been built that can be turned on and off with a nanowatt of power from three feet away, with the concept being to use the nanoresonator itself as the antenna for the device The device achieved an efficiency of 15% and the group believes it might find application in optogenetics to provide a route for wireless power and communications to devices implanted in and interfaced to the brain. But such wireless MEMS could be used everywhere: for example a modified router might monitor wireless MEMS sensors placed on movable objects all over the house.

10. A Sewing Robot
Sewbo has launched a robot to automate garment sewing, such as the sewing that typically takes place en masse in sweatshops It doesn’t have the versatile flexibility of human sewing of course, and the key innovation is a method to temporarily hold the garment fabric in solid sheet form (it uses off-the-shelf sewing machines and robotic arms) that can be more easily picked up and guided by automated systems, but which when plunged into warm water removes the polymer to return it back to the soft flexible garment for sale and use. This gets us towards fully automated garment production.

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Ethereum's Swarm Starts to Mature
Towards Web 3.0?

Ethereum’s blockchain contender for the distributed web, called Swarm, is starting to mature and its transformative capacity is becoming clearer - as covered by this recent Coindesk piece

I first covered Swarm in May this year, outlining the benefits of using the Etherum blockchain for domain name resolution and coordinating the other necessary storage and communications infrastructure needed for running a distributed web.

The Swarm testnet is now live and if successful will provide a platform for decentralised uncensorable hosting of photo albums, file managers, web sites, blogs, social media networks, and just about anything for which you rely on the web’s current centralised server model. This is one of the reasons I continue to think Ethereum remains an interesting investment to consider.

Ethereum and ETH provide the computational tools, Swarm and the Whisper protocol provide basic web infrastructure, while new tools Swear and Swindle are smart contracts that aim to ensure stored data remains available to users. In this arrangement you don’t store data on the blockchain - instead Swarm embeds references to that data on the blockchain as a storage layer or pointer to where that data resides.

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Actually Gad I think the use cases go far beyond what you may be thinking. Any site that uses version control may use IPFS/SWARM. Version control typically saves each copy as a record (for rollback, history) with diffs between. These are all static pages. Each could be content (not location) addressable aka IPFS / SWARM.

Consider Github, which is the genesis of IPFS... it's only apparently a dynamically changing site with static pages at the file level.

SO many services would be improved using content addressing. Twitter, Facebook like social media, most webistes, all 'oracle' services like stock market feeds, etc.

At first blush it seems a waste to store each page and subsequent frequent edits as statsi content but yet thats wht so many business, not to mention security and government agencies due. How many copies of twitter feeds are out there so you think... tens, hundreds. How about just one sotred via IPFS that all could access and do analysis there on. Its not theory, there is already a tool to stream twitter feeds to IPFS. So much more to come...

The impact and new capability from a true permanent irrefutable record of communication will be profound for commerce through to crime analysis on to social science analysis of culture, etc.
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SciTech #ScienceSunday Digest - 38/2016.
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Beating neurological damage, Delivering bacteria, 3D electodeposition, Multicore computing accelerations, Fruit fly connectome, Characterising cell senescence, Novel semiconductor nanostructures, Nanoscale motion amplification, Machine learning tricks, Bonding etched metals.

1. Compensating for Neurological Damage
A new brain computer interface allows patients to control the movement of a cursor over a keyboard with just their thoughts, and by so doing type 12 words per minute The tests were carried out in monkeys but should translate well to people, and achieved a significant improvement in the rate of word transcription over previous systems to be conversationally useful. In other news recent quadriplegics might have significant limb movement restored by having 10 million (particular type of) stem cells injected into the site of spinal injury, to the extent that three months later patients can feed themselves and operate their phone.

2. Controlled Bacterial Delivery to Intestines
A delivery method comprising alternately coating bacteria in layers of long chain polysaccharides chitosan and alginate, ensures their protection against stomach acids and into the intestine where these mucoadhesive sugars help adhere to the intestinal lining Coated bacteria had a survival rate six times higher than uncoated bacteria. Such improved oral probiotic delivery to the intestines could be widely beneficial considering the number diseases and treatments probiotic and even therapeutic bacteria are being proposed for.

3. Electrodeposition vs 3D Printing
The custom mass-produced devices create by Microfabrica’s electrodeposition technique are very impressive Microfabrica’s process represents a synthesis of 3D printing capabilities with semiconductor electrodeposition fabrication techniques, and this enables a much greater level of device and scale precision - check out the comparison images with conventional metal sintering for example. The company is already commercially operational and sells devices for $1 - $100 depending on size and complexity.

4. Language & Hardware for Accelerated Computing
Milk is the name of a newly developed programming language that manages memory much more efficiently in programs that deal with scattered data across large data sets, so much so that it enables a four-fold speed-up in big data applications The Queue Management Device designed by Intel reduces certain optimisation software to a chip-based hardware design that at minimum results in core-to-core communication speed multi-core chips to be doubled

5. Fruit Fly Connectome
The first complete 3D map of a fruit fly brain connectome has been assembled This approach used x-ray tomography and worked by soaking the brain in a silver dye, then bombarding it with x-rays, measuring the x-ray scattering, and running the data through a computational model to generate a 3D map of neurons and their connections. This model has a resolution of 600nm and shows 100,000 neurons and is the first ever reproduction of a fly brain hemisphere mapped with 3D coordinates. It took 1,700 man hours to assemble so will need further automation if the technique is to tackle larger brains.

6. Characterising Genetic Causes of Cell Senescence
Recent work looked at dosing varying levels of a certain anti-cancer drug against cancer cells in order to induce varying cellular responses from senescence to apoptosis; in doing so identified 25 specific genes responsible for the senescent cell response as opposed to apoptosis or other responses Identifying these 25 genes provides 25 possible targets that can be investigated for targeting specific senescent cell clearance therapies - which some companies are already working on - in order to help rejuvenate aging tissues and reduce the age-related load of senescent cells.

7. Novel Semiconductor Nanostructures
An inorganic semiconducting material with a double helix nanostructure has been discovered, comprising non-toxic tin, iodine, and phosphorus, has been formed into centimerter-long fibers and possess exceptional flexibility while remaining stable at up to 500C. In related news quantum dot silicon nanoparticles can replace alternative semiconductor materials in a range of useful applications in displays and optoelectronics

8. Nanoscale Motion Amplified to Microscale
A microelectromechanical system developed by NIST is able to measure the transfer of motion at nanometer scales As long as the electrical input driving the system was free of noise then the device performed reliably and repeatedly, and offer a platform that the team hopes to extend to far more complex systems with many moving parts. Advances like this have application in fabricating and operating various micro- and nanoelectromechanical systems used in sensors, switches, and automatic robotic systems.

9. Latest Machine Learning Tricks
Machine learning algorithms for driving autonomous vehicles are being accelerated and rapidly tested in consumer video games such as Grand Theft Auto, taking advantage of realistic environments, and enabled by a new way for extracting useful training data from the game environment for automatic object classification Machine learning algorithms are now generating short videos from static photos, aiming to predict what happens next in the scene captured in the image, take a look for some “interesting” results.

10. Bonding Metals with Any Other Surface
A new electrochemical etching process produces metal surfaces with roughened micrometer scale features that allow metals to be joined with nearly all other materials, become water repellent, and exhibit improved biocompatibility The etching process affects only the top 10 - 20 micrometers of the surface, removing those metal grains that are less chemically stable, creating a complex three dimensional surface that can be strongly bonded with polymer adhesives to connect other similarly-etched metal surfaces; in tests the metal or polymer would break before the interface. In thinking about the laminated wood being considered to build wooden skyscrapers because of its strength, I’m wondering about laminated interleaved metals and what you might build with them?

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cool set )
except that #2 may have more military application..
About #6 - have read somewhere, that more than 90% of death causing metastases are created by tumor cell colonies, moving/walking through the tissue, not by bloodflow as supposed before.
Interesting if there are genes, that would block these colonies, prevent them from moving? Addressing this area seems to be promising.

talking of #10, specifically of wooden skyscrapers - don't think that's a good idea: minor damage to laminating cover (windows washers, construction work, falling objects, small drone impact or accidental bullet from the street) - and construction element is all open to weather, mushroom infection, etc. And because of same metal coating no one predict, when it cracks, resulting picture similar to 0911 WTC fall.
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SciTech #ScienceSunday Digest - 36/2016.
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Nanowires in mouse brain, Neuronal pixel interface, Custom molecular cages, Giant macrodimer molecules, Boosting neurogenesis, Antibody clears amyloid, Carbon nanotube transistors, Universal cancer investigation, Atomic deposition techniques, Centimeter accurate GPS.

1. Mouse Brains Monitored with Injectable Nanowires
Very thin flexible silicon wires coated in polymer form a mesh of simple field effect transistors that can curl up, drawn into a syringe, and injected into mouse brains where they can record electrical activity from individual neurons The mesh functioned well throughout the entire 8 months of the experiment by avoiding the immune response and scar tissue formation that plague other systems. They were able to record and measure changes in the mouse brain and even tracked individual neurons for long periods of time. Some of the electrodes could provide stimulation to neurons and this opens up avenues for very interesting digital interfaces.

2. Neural Pixel Interacts with Tiny Brain Regions
A tiny 20x20 micrometer device called a neural pixel consists of a sensor that detects neuronal signals and an ion pump that doses a tiny amount of the neurotransmitter GABA In this case the device detects neural cascades associated with epilepsy and doses GABA to inhibit and stop that activity from spreading - admittedly only in slices of brain at the moment. The possibility of including other drugs and neurotransmitters and placement in different brain regions makes this a genuinely interesting platform. It’d be interesting to combine this with #1 above. It’d be even more interesting to integrate a third, regenerative device that takes in nutrients from the surrounding tissue to produce GABA (in this case) to replenish the tiny reservoirs so it can operate indefinitely.

3. Custom Molecular Cages
First, custom proteins are being developed that function as microcompartments for custom catalytic applications, and in this case internally incorporated catalytic iridium and palladium complexes that catalysed hydrogenation and cross-linking reactions Second, a method has been developed for synthesising (via self assembly) custom covalent organic nanotubes out of simple organic monomers that are stabilised by light-induced cross-linking Both interesting platforms with a wide range of potential applications depending on the needs and materials used.

4. Giant Macrodimer Molecules
Diatomic molecules, or two-atom dimers, have been created from cesium atoms that are space one micrometer apart from one another This comprises experimental confirmation of a decade-old theoretical prediction, although the dimers only exist for tens of microseconds. Depending on the state of the atoms and the distance between them the force they experience can be attractive or repulsive. This was all done by firing lasers at an ultracold gas of the atoms, with the lasers putting the atoms into the correct state, and so forcing the dimers to form to reduce their total energy.

5. Boosting Neurogenesis in Old Brains
A couple of new molecular techniques have been discovered for temporarily and intermittently boosting neurogenesis (creating new neurons) in older brains In this work the expression of certain proteins important to dendritic spine maintenance were altered, removing a portion of spines of old neurons, and resulting in neural stem cells being activated and doubling the number of new neurons that integrated into the region, and when turned off the old spines grew back. Mice in these experiments exhibited improved memory function.

6. Antibody Clears Amyloid from Human Brains
The results of a human clinical trial involving 165 people have demonstrated that an antibody effectively binds to amyloid plaques in human brains, mobilises microglial immune cells to remove and destroy the plaques, and almost completely clears the brain of plaques within a year The cognitive decline suffered by the Alzheimer’s patients slowed significantly. More patients and continuing, longer trials should soon answer the question of the cause-or-symptom nature of amyloid in Alzheimer’s disease, although this work is promising. Similar techniques may quickly be adopted from this promising approach to create treatments for clearing tau protein and other protein clumps that contribute to disease and decline.

7. Carbon Nanotube Transistors Surpass Silicon
New carbon nanotube transistors can carry nearly double the current of silicon transistors This work involved depositing aligned arrays of carbon nanotubes on a 1-inch square wafer in order to form transistors coating the entire surface in less than five minutes. One of the key advances was new abilities to remove the vast majority of carbon nanotubes in order to achieve 99.99% semiconducting carbon nanotubes. There are more and more advances like this and it seems as though carbon nanotube transistors are starting to mature. Meanwhile Fujitsu looks set to launch carbon nanotube RAM chips by the end of 2018

8. Telomerase and ALT Universal Cancer Investigation
Recent work is helping to determine how cancer cells switch from an activated telomerase mechanism of increasing or maintaining telomeres to the Alternative Lengthening of Telomeres (ALT) mechanism that 10% - 15% of cancers are driven by Successfully targeting and treating both telomerase and ALT -based mechanisms provides the promise of being universally applicable to treating any and all cancers due to this fundamental mechanism being crucial to cancers growing beyond a small mass of cells and metastasising. Unlike telomerase in stem cells, ALT is not used by any normal adult cell and so can be deactivated systemically with little effect.

9. Room Temperature Atomic Deposition
DARPA has developed the electron-enhanced atomic layer deposition technique that enables the room-temperature synthesis of ultra-thin-film microelectronics materials Previous techniques have demanded temperatures over 800 degrees celsius to produce these types of films, but superior capabilities at room temperature now allow previously infeasible device and material compositions to be designed and created, and the ability to selectively etch different materials in composites provides an alternative to typical masking techniques.

10. GPS Accurate to the Centimeter
A new software-based system running on a Raspberry Pi and totalling $35 worth of hardware provides cars with centimeter GPS accuracy The system does demand a network of ground-based network stations positioned no more than 20km apart (closer for built up areas) to help improve the accuracy and timing of GPS, but the utility of such accuracy to autonomous cars, trucks, drones, and other devices is obvious. The system has been successfully tested on smartphones but is unlikely to be rolled out to new smartphone devices in the foreseeable future due to added extra costs of antennas and power.

Also: SciTech Digest was mentioned in a new Podcast last week by Spark Vizla

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6 made the BBC evening news, which was good to see. It certainly seems highly positive.
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CS Lewis' Humanitarian Theory of Punishment

This is CS Lewis' (the Narnia author) essay on the Humanitarian Theory of Punishment[1] and is wonderfully narrated and animated by the CSLewisDoodle channel[2]. This essay argues a critique of the humanitarian (as opposed to retributive) theory of punishment and presents a range of interesting ideas and concepts on criminal justice that I hadn't explicitly encountered before. I found it interesting as the first criticism I've ever heard of humanitarian punishment being potentially unjust and immoral.

There are several key words or sentences in the presentation that may trigger objections or counter points, and the positions put forth by Lewis are not without criticism[3]. But overall I found it interesting, as an atheist, that I'm able to appreciate - if not completely swallow - the positions put forth by a prominent Christian apologist. The style of writing or wordsmithing is itself excellent, and of a sophistication that we may have lost.

The essay on subjectivity[4] is also very good for similar reasons as it forces you to think about and question some fairly fundamental things from a perspective that you may not have encountered before.

1. Main video
2. CSLewisDoodle channel has a library of these essays.
3. Selected criticisms
[4] The Poison of Subjectivity

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+Mark Bruce that's a really good one! I must have read that essay back when I was reading Lewis a lot, because I looked for it when I was raising my son, but couldn't remember the author.
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Modern Day Cults can Wield Considerable Influence

This is an excellent presentation and blog post reviewing a book that resulted from the psychological study and research of cults and cult-like behaviour. There were a number of times when I felt chills down my spine while listening, as I realised that the behaviour and actions being discussed were descriptive of influential mainstream groups, organisations, and movements in the real world today. Some of which wield considerable cultural and political power.

Also, we’re all a little bit cultish in our behaviour and even if that typically doesn’t manifest to the extent of actual “cult membership” it is more prudent, more necessary, and more important than ever to question one’s beliefs regularly and deeply. Deliberate exposure to ideas and content outside of your typical media consumption and social exposure can make this necessary process easier.

I’ve started to wonder if the dynamics of the Internet and the media consumption behaviours it encourages in all of us actually serve to exploit the idiosyncrasies of human psychology to make the formation of cults and cult-like behaviour much easier, and much more effective than we really appreciate. The filter bubbles. The echo chambers. The self-righteous morally outraged victimhood culture. The politics of the other. The suppression and censorship of dissent. All feedback powerfully one on the other to make modern day cults that much more powerful, invisible, and pervasive.

Groupthink, wrongthink, and doublethink are all endemic to cults.

Selected Excerpts

Here’s a selection of key excerpts if you don’t have time for the entire presentation, which lasts for a bit of 30 minutes, or for the blog post, which is lengthy. But I’d encourage one or the other if you can manage it.

The structure of cults is basically authoritarian; obedience and hierarchical power tend to take precedence over truth and conscience when they conflict, which they often do. Unfortunately, certain psychological benefits can make authoritarian groups very attractive – they provide the opportunity to feel protected and cared forIntelligent, well-educated people join cults because they simultaneously desire a sense of working for a higher purpose and because they are afraid of being on their own.

What I wish to stress is not that every group is a cult, but that cult thinking is the effect of psychological forces endemic to the human mind, and that these forces operate in the everyday life of each of us; they distort perception, bias thinking, and inculcate belief … and while not all cults require a formal leader as such, the authority figures … empower the group by giving them a source of confidence and righteousness that enables them to delegitimise dissenting points of view through their air of authority.

Projection offers protection from the anxiety of being bad and the punishment of being abandoned. In addition, by making other people bad in our own mind, we can legitimise behaviour toward them that would otherwise be morally unacceptable, even to the point of sanctioning cruel and vicious actionsProjection is is infused with self-righteousness to increase moral security. If the group member represents all that is good and the outsider represents all that is bad, it is natural to feel morally superior. It allows the group member to separate the world into a false dichotomy in which they have chosen the sacred path and the path the outsider has chosen is profanePerhaps the most important thing to understand about devaluing the outsider is that it is a necessary preliminary to harming others, to doing violence.

Only a lively appreciation of dissent’s vital function at all levels of society can preserve it as a corrective to wishful thinking, self-inflation and unperceived rigidity.

A cult is a group fantasy created and maintained around specific beliefs for the emotional protection of its members. If information or opinions exist that contradicts the dogma or goals of the group, the only protective measure the group can take is suppression. Thus the core philosophy of the group becomes rooted in the distortion, if not outright fabrication, of reality. This censorship does not have to be as overtly authoritarian as one might imagine.

Care to suggest any groups this reminds you of?

Main video:
Blog transcript:
Second video: - this covers case studies of actual cults and is also worth a listen.

Matthew J Price's profile photoTim Stoev's profile photoJason Anderson's profile photoMark Bruce's profile photo
Aye +Jason Anderson, the various offshoots of progressivism seem to me to be the most insidious and dangerous cults operating today. More so because their tactics are more sophisticated, exploiting altruism to turn it against itself. 
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Godzilla’s Presuasion

In this little video famed psychologist Robert Cialdini presents the basics of presuasion, a bunch of methods used to prime people to receive your message more favourably and so increase your probability to successfully persuade them towards some desirable outcome. I’ve been waiting for Cialdini’s Pre-Suasion book to launch for a while now and it “happens” to have coincided with the release of this video by BigThink; I’ve just gone and grabbed the ebook version.

Cialdini’s Influence: The Psychology of Persuasion is probably one of the best human psychology books that I’ve ever read and I’d highly recommend it to anyone who hasn’t heard of it or read it before. It seems that Pre-Suasion will be a good follow-up or companion book with useful tips and lessons for many if not all areas of life.

Remember: these types of psychological methods are not aimed solely at helping you influence others, but just as important to help you be aware of and recognise when these methods are being used on you.

Scott Adams (of Dilbert fame) refers to Cialdini as Godzilla, as in “the Godzilla of manipulation, influence, and persuasion” and suspected secret strategist to Clinton. Apparently Cialdini was an advisor and strategist for the Sanders campaign and shortly after Bernie pulled out of the race Clinton’s campaign started using very similar tactics, somewhat different to what they had deployed previously.

BigThink is a pretty cool YouTube channel with quite a bit of regular content and interesting interviews with different people. Worth checking out if you haven’t already. 
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+Mark Bruce what if we could erase some of our good memories ?
Conscious thought ! what do u think ?
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The Neural Network Zoo

This is nice summary article covering the many different neural network architectures that have been developed and deployed in deep learning applications. The taxonomy provides a colour-coded key to make it easy to see how different functions and operations are used in different ways across different network architectures and so showing at a glance how these different networks relate to one another. The article provides a brief description of the function and training of each type for ease of classification and reference.


We can expect this taxonomy of different neural network architectures to grow over time too: as our knowledge of the brain and understanding of its different neural networks continues to become more sophisticated we’ll undoubtedly discover new network architectures as well as refinements that will be useful to replicate in artificial neural networks and deep learning applications.

Via +Cristian Lorenzutti
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Kakvo e tova
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SciTech #ScienceSunday Digest - 37/2016.
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Sand into soil, Optical soliton waves, Microbiome tissue repair, Stem cell gun, RNA genome regulators, Prion structures, Deep learning speech, Thermal solid superatoms, Sophisticated drones, Synthetic wine.

1. Turning Sand into Soil
A formulation of plant cellulose added to sand helps the mixture retain water, nutrients, and air, with sandy hectares of land in Mongolia treated with the mixture proving successful in trials by growing rice, corn, tomatos, watermelon, and sunflowers This would be interesting not just for turning deserts into productive agricultural land, but also facilitating the recovery of native vegetation and forests onto desertified land, rejuvenating tired soils and even, at a futuristic stretch, helping to terraform the surfaces of other planets.

2. Optical Soliton Waves
A new optical phenomenon has been observed for the first time in the form of a new type of soliton wave I’ve always found solitons fascinating; localised waves that act as particles, holding their shape as they travel instead of dispersing like standard waves. This new phenomena involves soliton waves riding the wake and path of another soliton wave, and the group can design microcavities to guarantee the properties of the solitons that will be produced; applications include optical clocks, navigation and radar systems, magnets, neurobiology, and fiber optic signalling generally.

3. Microbiome Impacts Tissue Repair and Regeneration
Recent work on very simple animal model organisms suggests a link between an organism’s microbiome and its immune system and ability to repair and regenerate its tissues Different microbial populations in the organism can significantly inhibit or enhance the processes of tissue repair and regeneration, and the immune system plays a key role in this, for example sometimes blocking regeneration if an infection is present. While yet to find similar definitive links in humans potential applications include: new drug candidates for boosting repair and regeneration and avenues to explore the creation of healthier and more beneficial microbiome populations.

4. Gun that Shoots Stem Cells
A SkinGun device developed by RenovaCare uses the company’s CellMist system to spray a patient’s own stem cells onto skin wounds in order to rapidly speed up repair and regeneration of skin in days instead of weeks While it won’t work for third-degree burns and very deep wounds, it is effective against second-degree burns and other infected wounds. I also wonder if such an approach might facilitate a type of skin rejuvenation treatment in future, as well as modified versions able to repair the surfaces of internal structures such as lungs, stomach, intestine, etc.

5. New Genome Regulation from “Junk DNA”
A new type of RNA called long noncoding RNA (lncRNA) that is transcribed from what was thought to be “junk” DNA and which does not produce proteins, has been found to play crucial roles in cellular processes and genomic regulation and gene expression In this work the structure of just one type of lncRNA was deciphered, which showed how this RNA structure is crucial to interacting with a specific protein to control the development of heart muscle cells. The work was done in mice, and while human and mouse proteins are usually similar lncRNA sequences are not conserved and the human counterpart in this case has not yet been found. The group hope to build a library of lncRNA structural motifs to push the field forward and help identify targets for disease.

6. Deciphering Prion Structure and Replication
In related structural biology work we have recent advances in understanding prion structure, formation, and replication, and how this new evidence refutes conventional theories of this process In the case of normal protein PrPC that can turn into misfolded infectious prion PrPSc and recruit normal versions to replicate itself, it was shown how these molecules self assemble two intertwined protofilaments that create the fibrils that are typically observed. At a basic level these misfolded proteins comprise repetitive elements of beta-sheet structures - four-rung beta-solenoids - that act as templates for new, unfolded proteins build on. It is hoped this understanding will help quickly understand other prion diseases and the development of therapeutics.

7. Deep Learning for Speech Production
Google’s DeepMind has demonstrated WaveNet, a deep learning system for generating speech that mimics any human voice while sounding more natural than any current speech-to-text system and reducing the gap between human performance by over 50% The system can also synthesise music and automatically generate sample piano pieces. All of the examples are well worth a listen, including when the system makes up words and changes the identity for the same text. In related news physicists are exploring why deep neural networks are so effective at solving complex problems and how this is linked to fundamental physics

8. Superatoms: Thermal Solids & Precise Clusters
Crystals comprised of superatoms of buckyballs and similar-sized inorganic molecular clusters exhibit variable, controllable thermal conductivity depending on whether the buckyballs are fixed and ordered (high conductivity) or rotationally disordered (low conductivity) Adding magnetic properties to the superatoms might allow thermally switchable materials for example, and a range of complex yet tunable atomically precise structures. In related atomically precise materials news, the largest ever atomically precise silver nanoclusters have been synthesised and characterised, containing precisely 374 atoms in a 3nm core surrounded by a layer of silver atoms bound to thiol molecules

9. Interesting Drone Capabilities
First, effective designs for low-power autonomous robotic sailboats are now scouring the oceans collecting data and accessible remotely Second, software is getting far more sophisticated at allowing swarms of robotic drones to coordinate and adaptively avoid collisions Third, tree-planting drones are being used to speed up reforestation efforts Finally, drones are being fitted with anti-laser lasers to avoid being shot down

10. Synthesising Artificial Wine
Ava Winery is a company that appears to be getting very close to creating convincing synthetic artificial wine that can fool any human taster Wine is about 85% water and 13% alcohol plus a range of hundreds of other molecules that provide flavour, aroma, colour and other properties. Earlier this year 80% of people could differentiate between a control glass of wine and a glass of the artificial wine; as of today only 10% of people can and this is set to get smaller. There are many benefits here, aside from using 50x - 100x less water to produce the wine, the possibility of powdered wine mixed with water/ethanol solution, and generally disrupting the wine industry and others.

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Adam Black's profile photoХйер Хит's profile photoJames Field's profile photoMark Bruce's profile photo
Just a couple of ideas +James Field - RE your thoughts in #7, perhaps the training on many speakers helps the system learn what features to exclude in order to better simulate one speaker alone, information that would be unavailable if it was just learning from that lone speaker?

As always, love your additional commentary and insightful points, cheers!
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SciTech #ScienceSunday Digest - 35/2016.
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Dopamine gene therapy, Remyelination cell therapy, Algebraic brain topology, Ginko custom microbes, Ultrasound protein imaging, MegaMIMO bandwidth boost, Thought activated DNA-bots, Light controlled CRISPR, Whole transparent organisms, Massively multicore chips.

1. Gene Therapy for Dopamine Production
A new treatment for Parkinson’s Disease is currently entering human clinical trials that involves genetically engineering the neurons of patients by administering large amounts of viruses that carry genes to better enable the brain to produce and manage dopamine Early results with initial patients show promise, not only for restoring cognitive function, but also for circumventing the main drawback to conventional L-Dopa and dopamine treatments which is the development of resistance and the need for ever greater amounts of drug that has less effect. There are currently 48 human clinical trials underway for brain and CNS gene therapies and cell treatments.

2. Cell Therapy Boosts Remyelination in Brain
A cell therapy product incorporating macrophages and microglia is showing promise in animal studies for remyelinating neurons in the brain and actively reversing the demyelination associated with many diseases including Multiple Sclerosis Such a treatment might not only be used in treating various neurological diseases but administered on a routine basis to restore myelin levels to youthful states as desired.

3. Understanding the Brain with Algebraic Topology
Mathematical tools from the field of algebraic topology are being used to better characterise and understand the structure and function of the brain and its connectome These new tools provide a different way of classifying nodes and loops, and for identifying these features at small and large scales. It should only be a matter of time before these additional tools and insights are incorporated into artificial machine learning systems.

4. Ginkgo Bioworks’ Custom Engineered Microbes
Synthetic biology company Ginkgo Bioworks continues to grow and develop custom genetically engineered yeasts that metabolise standard feedstocks under standard fermentation conditions to produce a range of different fragrances, flavours, cosmetics, and pesticides The company has scaled up, building a large automated foundry dedicated to rapid prototyping and rapidly generating custom yeasts to design specifications. These industrial synthetic biology facilities are starting to proliferate and at some point we can expect their capabilities to distributed to end users.

5. Engineered Proteins for Ultrasound Imaging
Newly engineered protein-shelled nanostructures known as gas vesicles, which reflect sound waves, can now give off far more distinct signals, target specific types of cells, and be used to generate “colour” ultrasound images Swapping and modifying different proteins on the surface of the vesicles alters cell targeting, molecule targeting, and sensitivity to different ultrasound frequencies. Such devices can be injected wholesale into an animal for medical imaging purposes, or a gene therapy could deliver the code to cells needed to produce the vesicles from scratch. Applications include e.g. using ultrasound to produce overlapping images showing tumour cells, the immune cells attacking them, and the vascular cells supplying nutrients. I also wonder if these vesicles might be co-opted to facilitate respirocytes.

6. MegaMIMO Boosts Network Bandwidth
The MegaMIMO wireless data system has recently demonstrated three times faster bandwidth and twice the wireless range of conventional Multiple-Input Multiple-Output systems The system manages to synchronise transmitter phases to coordinate multiple access points at the same time on the same frequency without creating interference and in order to maximise the efficient utilisation of the available spectrum. Such a system should provide needed boosts to both cellular and WiFi communications.

7. DNA Robots Activated by Thoughts
This is an interesting if somewhat convoluted proof of concept for triggering the activation of DNA nanobots in a living animal just by thinking In this system (i) an EEG headset records and recognises particular mind states, (ii) particular mind states influence the strength of an electromagnetic field, (iii) the strength of the electromagnetic field heats up metal nanoparticles injected into an animal (the subject themselves or another), and (iv) past a certain threshold the heated metal nanoparticles cause programmed DNA origami structures on their surface to reversibly activate. In this case they proved that the DNA nanobots were able to induce a cellular effect.

8. Modified CRISPR Controlled by Light
On the topic of controllable nanobots, the CRISPR system is being further engineered and modified to produce versions that can be controllably switched on and off in different ways Some approaches modify the Cas9 enzyme itself to achieve this, but the present work builds on earlier approaches that engineered light-activated RNA interference in order to produce modified RNA guide strands that are only activated in the presence of certain wavelengths of light. This allows precision experiments for controlling the precise timing of gene editing and other cellular signalling events. Next steps are exploring therapeutic applications and improving the design with a more universal system.

9. Making Whole Organisms Transparent for Imaging
Continual improvements and refinements in imaging and chemical techniques for making organs transparent have resulted in methods that can now make entire organisms transparent while labelling almost any desired internal structure for imaging and analysis In this work with the new uDISCO technique whole rats were rendered transparent and their nervous systems labelled with fluorescent tags in order to produce high resolution images and maps of entire neuronal networks with subcellular detail while still embedded in their original tissues.

10. Massively Multicore Chips
The KiloCore chip contains 1,000 independently programmable processors was fabricated by IBM The chip can process 115 billion instructions per second while dissipating just 0.7 Watts and has a number of novel features for applications including encoding/decoding, video processing, encryption. In related news a 25 core chip called Piton that is designed to more efficiently power massive cloud computing architectures Piton is designed to be scalable and so chips with thousands of cores and data centres with half a billion cores are envisaged.

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Wow, CPUs are getting ridiculously efficient!
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The Moral Roots of Liberals and Conservatives

Do you really, honestly, truly wish to better understand the world and your fellow man? To do so we need to break out of our limited moral matrix that dictates the lens through which we view the world and take a red pill, step outside of our comfort zone and take a renewed look at reality.

I thought this talk[1] by Psychologist Johnathan Haidt was so insightful that I should transcribe and summarise his presentation; when watching just be aware that it is presented to a particular audience.

I think presentations like this are crucially important for wider dissemination and consideration, especially in today’s toxic political climate. This toxicity usually stems from moral self-righteousness and a terribly tribalistic us versus them mindset. It births simplistic, outrageous, and misleading commentary on political candidates and political movements everywhere and one wonders if this might at some point threaten the very democratic process that has made all we have achieved possible.


The worst idea in all of psychology is that the mind is a blank slate at birth; the initial organisation of the brain provides a first draft that experience then modifies. This initial first draft provides five core moral predispositions along particular axes:

1. Harm/Care
2. Fairness/Reciprocity (Golden Rule)
3. Ingroup/Loyalty
4. Authority/Respect
5. Purity/Sanctity

This initial first draft of human morality, present in the new human, is going to be altered and influenced depending on the environment that human grows up in. Regarding #3, the Ingroup/Loyalty measure, humans are the only animal that forms groups much larger than the family. This stems from our long tribal history, and is driven by a tribal psychology that is so deeply pleasurable that even when we don’t have tribes we go ahead and make them anyway. My post on cults from yesterday relates to this.

To study these five factors Johnathan’s team used to collect measurements from a sample population of 30,000 people, and you can go a fill out the questions to see where your own morals fall as compared to everyone else. There are two very distinct categories that liberals and conservatives fall into; basically liberals believe morality only includes Harm/Care and Fairness/Reciprocity, while conservatives believe morality also includes the other three categories of Ingroup/Loyalty, Authority/Respect, and Purity/Sanctity.

The most important thing for those espousing only a two-channel morality is to understand why those espousing a five-channel morality believe that the other three channels matter. And in reverse, why the other three are discounted by those driven mainly by the two.

Conservatism is Important Because Order Tends to Decay
Cooperation with strangers and tragedies[2] of the commons are crucial problems that need to be solved by any successful and sustainable society, and the only way to do so is to enforce punishment of transgressors and cheats. Relying on people’s good motives is simply not enough, and those groups employing this strategy will fall into decline and fail. Interestingly, as an adaptation religion turns out to be very good at enforcing and incentivising prosocial behaviour.

The creation and maintenance of our civilisation necessitates the deployment of our entire moral toolbox, all five channels, in order to see the bigger picture and even have the hope of achieving higher, nobler outcomes. Order is desired even if it is sometimes unfair to some, and rampant diversity is suspect as it can lead to conflict and chaos.

Liberalism is Important as a Check to Oppression
Liberals reject the three channels and value diversity over the ingroup, disavow authority, and reject controls over what people can do to their body. This is often driven by noble motives as traditional morality can sometimes be oppressive and restrictive to individuals or groups. Change and justice is sought even at risk of losing order to chaos.

The fact is that order is very hard to achieve and very easy to lose.

Our morally righteous minds were designed to unite us into teams, set us against other teams, and blind us to the truth . . . because on issues of morality everybody thinks they are right. The goal needs to be to avoid self righteousness at all costs and to cultivate moral humility.

If you want the truth to stand before you, never be for or against. The struggle between “for” and “against” is the mind’s worst disease. - Sent-ts’an

1: TED presentation

Michael Powell's profile photoDeen Abiola's profile photoMark Bruce's profile photo
And around and around we go. Thanks both for your considered time and effort here. Seriously. Always interesting. Always challenging. Always makes me wonder how much more productive these things would be face to face with devices to hand.

+Michael Powell - if you look at the notes on the 29,000 figure site it admits that independent verification by BBC researchers over a certain time period confirmed that they had under-reported the numbers. But that site has a certain methodology and only counts incidents past a threshold confidence level. 
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SciTech #ScienceSunday Digest - 34/2016.
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Purifying carbon nanotubes, Anti-inflammatories for Alzheimer’s, Jumping robot legs, Protein sweeteners, Fortified GMO rice, Uber launches autonomous cars, Bacterial conducting nanowires, Superconducting electron superfluids, CRISPR for EvoDevo, Massively engineered genomes.

1. Purifying Carbon Nanotubes
One of the biggest obstacles to developing carbon nanotube applications is separating mixtures of carbon nanotubes to obtain pure samples of either metallic or semiconducting nanotubes depending on the requirements of the application. A new method for doing this involves a newly engineered polymer based on a template that was able to wash away semiconducting carbon nanotubes to leave metallic versions for use, but is now able to selectively wash away metallic carbon nanotubes to leave semiconducting versions for use Next step will be to make more efficient polymers and scale up production.

2. Anti-Inflammatory Drugs Treat Alzheimer's
Recent work shows that certain types of common Non-Steroidal Anti-Inflammatory Drugs are effective in treating Alzheimer’s disease in animal models by completely reversing memory loss and brain inflammation Next steps will be to confirm that the effect carries over to humans and, with these drugs already on the market for other NSAID-related indications, seek approval for repurposing in light of side effects.

3. Explosive Jumping Robot Legs
A new “GOAT” robot leg design is capable of explosive jumping to twice its height that can also walking, running, and compliant landings Next step is to improve the hardware then mount the legs onto both bipedal and quadruped robots, which I think will be very impressive to see. In related robotic automation news, agricultural fruit and vegetable picking robots continue to get better with the demonstration of a new automated apple picker

4. Protein-based Artificial Sweeteners
A protein that occurs naturally in a West African fruit turns out to be 2,000 sweeter than sugar Producing the protein at scale for commercial uses has been problematic however, although in this recent work the use of genetically engineered yeast to produce larger amounts of the protein via fermentation is showing promise. A reliable source of protein-based, non-sugar, non-aspartame sweeteners would benefit the food and beverage industry by circumventing the different problems surrounding conventional sweeteners.

5. Engineered Rice Addresses Zinc & Iron Deficiency
A new type of genetically engineered rice that fixes and stores significantly more zinc and iron has been created that can improve the lives of those suffering from deficiencies, especially in the third world This is a similar approach to the Golden Rice that has been around for a while that was engineered to produce more Vitamin A. In this case the iron and zinc content of grains was increased from ~3ppm to 15ppm and from 16ppm to 45ppm respectively. Next steps are to introduce the rice for cultivation in Bangladesh.

6. Uber Introduces Autonomous Car Service
Uber and Volvo will introduce a driverless taxi service in Pittsburgh this month using a fleet of 100 Volvo vehicles This won’t be a general-purpose service, but will rather ferry passengers between fixed points of interest around the city and the collaboration will further develop technology and mapping resources. The cars will apparently include “safety drivers” in the cars for the first rollout, not only to intervene if necessary but also to condition customers to get comfortable with autonomous taxis.

7. Producing Conducting Nanowires with Bacteria
Genetically engineered bacteria can now be controllably harnessed to produce electrically conducting nanowires This builds on earlier work that first discovered and characterised the natural bacterial nanowires, which allowed the rational design of modified nanowires by rearranging amino acids into an improved architecture. The nanowires produced by the bacteria are protein-based, 2,000 times more conductive than natural counterparts, and measured 1.5 nanometers wide. Future applications include electronics, sensors, and as power conductors in microbial circuits.

8. Electron Superfluid Critical for High Temperature Superconductivity
Recent analysis of materials that perform as high temperature superconductors reveals that their atomic architecture facilitates the formation of electron pairs into an electron superfluid that flows without resistance Analysing different types of these copper oxide materials (that include lanthanum and strontium) showed that differences in transition temperature between materials are determined by differences in the density of electron pairs. This challenges conventional theories of superconductivity and is hoped that this better understanding will lead to the design of materials with much higher, room-temperature transition temperatures.

9. CRISPR Accelerating the Field of Evolutionary Developmental Biology
CRISPR is having a transformative effect on the field of evolutionary developmental biology by allowing experiments to not only be done that could never be contemplated before but by significantly accelerating the rate and progress of the field Recent work traced the gene changes required for (i) turning fins into feet, (ii) improving photoreceptors in butterflies to detect a broader spectrum of colours, and (iii) how crustaceans acquired claws. Future work will look to modify the genes and pathways involved in building chicken beaks to find the sequences required for building theropod dinosaur snouts; we might yet get our chickenosaurus.

10. Most Engineered Bacterial Genome
The most engineered and radically rewritten bacterial genome has been produced recently The synthetic genome was synthesised with 3.8% of the original genome edited to replace 7 of 64 codons with code that produces the same components and so create an organism that functions on 57 instead of 64 codons. This would not have been possible even a few years ago and represents the largest completely synthesised genome with the most functional changes; next step is to boot it up into a functional cell.

Bonus: Festo’s Fantastic Flying Robots.
The latest robots from Festo are always a pleasure to behold

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+Adrian Reef Do you have a theory on Superconductivity that can predict what alloys will yield room temperature results?
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Hi, I’m Mark. I am a unique selfplex of knowledgeable, technophilic, and insatiably-curious memes currently residing on organic wetware with a personable and engaging predisposition, which is acutely aware of being a small but furiously spinning cog in the great meme-machine built by the human civilisation. 
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