opsin

Light Work

Understanding more about the human brain’s estimated 100 billion interconnected nerve cells, or neurons, could help us develop new treatments for disorders such as Parkinson’s disease, autism, schizophrenia and epilepsy. One method of investigating brain activity is to genetically engineer an animal, such as a mouse, so that its neurons produce a light-sensitive protein, opsin. Neuron activity can then be triggered by shining light on the brain, once it’s exposed in the anaesthetised animal. The computer simulation here illustrates a light beam hitting clusters of opsin on a neuron surface. The resulting nerve signals can be detected in connected neurons by inserting tiny probes to measure the electrical and genetic activity inside them. Scientists have recently developed a computer-guided robotic arm to insert the probes with greater accuracy than previously possible.

Written by Mick Warwicker

  • Ed Boyden
  • MIT McGovern Institute and Sputnik Animation
Let's Go, Rick Steves, and Walking in London: A Review Comparing different travel guides for London

A good guide can be a total vacation save when you’re exploring an unfamiliar place with a time. First time visitors to London have not finished packing up that led to one or two good travel guides in their backpacks. But with so many choices, taking the right book can actually become one of the most frustrating travel planning: rails are some redundant, some compliment one another, some are complete, others are superficial.Let ’s Go London City guidebooks, Rick Steves’ Great Britain, and Andrew Duncan Walking London are three very different books that have distinct purposes. And while certainly not the only London guides worth checking out, there is a 99% chance that at least one of them suits your individual needs. Let’s Go is probably the hottest business travel literature in the world at this time. They have put out guides that are stylish, economical, and-with a new version published every year, timely and accurate. Their London City Guide is no exception. Within the 350 + pages of the book, you will find heaps of detailed advice on eating, drinking, nightlife, museums and galleries, shopping, transport and accommodation (including hostels, bed & breakfasts, and even living rooms. ) All this information is conveniently organized by district. Within the pages of the guide Let’s Go find one for maps, charts, maps and more maps. lines the streets of London sprawling, casual, old-meets-new can make navigation difficult, but you’ll be fine if you’re carrying the guide Let’s Go: the first 8 and last 31 pages are devoted entirely to the maps. Bottom, Let’s Go has some ‘advertising on its pages, some of which can be intrusive at times. And even more significantly, Let’s Go lacks personality. It 'full of practical information such as addresses, prices and hours, but it lacks that human touch that can be so comforting for a traveler in an unfamiliar place. This is where the game Rick Steves travel stories personal opinions frankly and historical curiosities to Rick Steves’ Great Britain a perfect companion to (or replacement) Let’s Go guide with a section entitled “Delusions of London, you know this guy is pulling no punches. But what really makes it stand out from Steves travel writer and his drawings. He insists that his readers get a visual representation of everything he writes. His guide is filled with easy to follow, hand-drawn maps of everything from entire regions, cities and districts, right down to floorplans of galleries, museums and castles. -And as you probably guessed from the title-Rick Steves’ Britain does not deal exclusively in London. The book covers all the best that England, Wales and Scotland have to offer. This makes it perfect for travelers who plan to spend time outside of London for part of their journey. Steves also publishes a guide of the city of London-specific, but with 80 + pages of the book in Britain devoted exclusively to London, why bother? My only problem with writing Steves’ is that while he certainly does not bear to throw away money, may not be enough for some budget-oriented travelers (like those on a student budget.) For example, his recommendations to address accommodation almost exclusively with hotels, hostels, giving only a hint. And while people in Let’s Go understand that you’re willing to walk eight miles for a cheap drink, Steves’ readers have to resign themselves to the idea that they are going to pay $ 10 for a beer. Last but by no means least, we strongly recommend checking out Walking London by Andrew Duncan. It ’s a very special book, not an all-encompassing guide to the city, but a manual step-by-step tour to 30 do-it-yourself walking through the most famous districts of the city. Even if you’re not one of the turns in its entirety, holding a copy of Walking in London stock exchange days is guaranteed not to miss important points of reference, good food, or photo opportunities as you are walking from place to place. Although I do not recommend using London as a tourist guide Walking alone makes it a striking partner for any of the most complete guides or country. If you decide to take it, I support the "Westminster and St. James 'and’ Bankside and Southwark” missed like two walks. Whatever you decide to go with books, there is an important secret to using them correctly: to study before you go. What better way to ruin a vacation than spending all the time with his face buried in a guidebook.


Farellones
Watch on moebrowntown.tumblr.com

Opsin

Ivan Villafuerte

Sin Are Acids In The Eyes

This guy was standing on a corner in Greenpoint, Brooklyn preaching about “the DNA of sin.” He told me, “Sin are acids in the eyes called OpSin…which form free radicals causing aging, disease, and death.” I think he also said his church sell anti-aging products. It was a lot to take in…

More photos of Preachers and Super Religious Folk and from the Random Strangers Series.

Octopus-Inspired Camouflage Flashes to Life in Smart Material! (TECHNOLOGY)

     Octopuses and their cephalopod cousins are the undisputed masters of disguise. An octopus can change its color, texture and luminosity faster than you can say “camouflage.”

     So far our lowly human attempts at imitation have been quite crude. But a flashy new smart material might just be our closest step yet.

     The main tool the octopus uses for its visual display is a cell called a chromatophore. These small, pigment-filled sacs expand and contract to create an array of colors and patterns. How does the octopus decide what colors and patterns to make? Recent research suggests that octopuses can also sense light—and possibly even color—through photo-sensitive cells (called opsins) in their skin.

     The idea of a material that can both sense and create visual change is quite appealing to science (and the military). Renowned cephalopod researcher Roger Hanlon, a senior scientist at Woods Hole Marine Biological Laboratory, and John Rogers, a professor of materials science and engineering at the University of Illinois at Urbana-Champaign (whose previous work includes flexible temporary tattoo-like circuits), teamed up with a crew of international researchers to create a changing heat- and light-sensitive sheet of pixels, described earlier this week in Proceedings of the National Academy of Sciences.

Photo sensible nanomaterial, based in octopus skin

More facts and Science in: www.newhorizonshept.tumblr.com

BMC

According to a study conducted by Brian Verrelli (a researcher at the Biodesign Institute), aye-ayes have the genes to see in color, even though they are completely nocturnal and have been for millenia. Why is this so significant? Verrelli and his colleagues study three genes in particular called opsins which are responsible for color vision in humans. Yet, aye-ayes are completely nocturnal.

Prevailing scientific wisdom follows a “use it or lose it” mentality, meaning over the past ~60 million years, the genes that allow for color vision in aye-ayes would degrade due to mutation, because the completely nocturnal animals would not be using color vision, and thus undegraded opsins would not be selected as an evolutionary advantage.

After studying the DNA of eight aye-ayes, however, Verrelli was shocked to find that the opsins of bizarre creatures are not degrading at all. “In fact,” says Verrelli in this article in Science Daily, “For the green opsin gene, we did not find a single mutation in it. The opsin genes look to be absolutely fully functional, which is completely counter to how we had believed color vision evolved in nocturnal mammals.”

The ramifications of this finding have yet to be fleshed out, but they have certainly turned conventional wisdom on its head, at least for the study of opsins. Verrelli hopes to join with animal behaviorists to determine if the aye-ayes indeed have the power to see in color by day or by night.

ILMEENI kun nuketown tulee black ops kolmoseen????

10 years of neural opsins

10 years of neural opsins

https://twitter.com/eboyden3/status/636288652319031296

Just in time for Nature Neuroscience’s Optogenetics 10-year anniversary retrospective, Ed Boyden has announced the first (?) time the FDA has approved optegenetics for human testing.

The set of retrospective pieces that NN published are quite interesting. For instance:

(Deisseroth) It seems unlikely that the initial experiments described here…

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CIRpy - A Python interface for the Chemical Identifier Resolver (CIR)

In the past I have used the ChemSpider API (through ChemSpiPy) to resolve chemical names to structures. Unfortunately this doesn’t work that well for IUPAC names and I found myself wondering whether it was worth setting up a system that would try a number of different resolvers. More specifically, I wanted a system that would first try using OPSIN to match IUPAC names, and if that failed, try a ChemSpider lookup. Just as I was about to start doing this myself, I came across the Chemical Identifier Resolver (CIR) that does exactly that (and much more).

CIR is a web service created by by the CADD Group at the NCI that performs various chemical name to structure conversions. In short, it will (attempt to) resolve the structure of any chemical identifier that you throw at it. Under the hood it uses a combination of OPSIN, ChemSpider and CIR’s own database.

To simplify interacting with CIR through Python, I wrote a simple wrapper called CIRpy that handles constructing url requests and parsing XML responses. It’s available on github here.

Using it is a simple case of copying cirpy.py into a directory on your python path. Here’s an example using the resolve function:

import cirpy

smiles_string = cirpy.resolve('Aspirin','smiles')

There are full details of all available options in the readme.

You Can Now Wirelessly Control a Mouse Using Optogenetics

Scientists at Stanford University have changed the game of optogenetics by making it wireless. You can now manipulate brain activity in mice without using a bunch of wires attached to their head.

What is optogenetics?

Optogenetics is a technique invented to manipulate brain activity using light. Developed in 2010, this method is used to study the activities of brain and spinal cord by mapping how they respond to light. As the name suggests, this uses a combination of ‘optics’ (light) and ‘genetics’ (genes). In order to make them sensitive to light, neurons are genetically modified to express light-sensitive proteins called opsins. Since its inception, optogenetics has revolutionized the field of (neuroscience); it has provided answers to pressing questions in the field of Parkinson’s, pain management, and stroke.

Find out more light tech in mice and memories!

The latest in optogenetics: wireless implantable devices

Traditionally, optogenetics uses fiber optic wires attached to the mouse’s head to deliver the light for stimulation. While this setup might work for a mouse in an enclosed cage, it is quite restrictive when studying mice behaviors like burrowing and interactions with other mice. Also, attaching the wires before every experiment disrupts their natural rhythm, possibly stressing them out. These factors could confound the results obtained for studies on mood disorders like depression or schizophrenia, which heavily rely on social interactions. The Bio-X team at Stanford University has found the perfect solution to unfettering the mice.

How does this device work?

Building the implantable light-emitting device wasn’t difficult for the scientists. Powering the device was. A localized power source that would track the mouse’s movements throughout the experiment was too bulky and would defeat the purpose. So, Dr. Ada Poon, one of the researchers on this team had the idea of using the mouse’s own body to power the device. Here’s how they made it work: they first built a cavity that could amplify and store radio-frequency energy.

In order to prevent it from getting out, they enclosed the cavity using a grid that had holes smaller than the wavelength of radio waves. This way, the energy stays trapped inside, except when something comes in contact with the grid⎯say a mouse. Since the wavelength of this light is the same as that would resonate in a mouse. Therefore, when in contact with the grid the mouse essentially acts as conduit channeling the radio frequency energy to power the light-emitting device. We now have a mouse powering a tiny device that can be implanted under the skin, and light up wherever the mouse chooses to go.

This wireless innovation will definitely make behavioral studies in mice easier and free from any confounding factors. Also, since we do not have genetically engineered neurons in our bodies, we don’t have to worry about these devices controlling our brains anytime soon.

Find out more about how mice help save lives!

On that light tech grind…

Katsomusaine(id)en tulevaisuus

Kansalaisaloite ( lue perusteluja esim. http://www.katsomusaloite.fi/kannattajat-1/) yhteisestä katsomusaineesta on saanut paljon intuitiivista ja osin pohdiskeltuakin kannatusta. Mietin seuraavassa, kuinka realistisia yhteiselle katsomusaineelle asetetut toiveet ja tavoitteet ovat - omasta kapeasta näkökulmastani.
Rehtorien ja taloutta ajattelevien näkökulmasta monet eri katsomusaineet ovat tuhlausta ja hankaloittavat opetuksen järjestelyä. Monissa kouluissa ei tosiaan onnistuta järjestämään edes elämänkatsomustiedon opetusta samaan aikaan kuin uskonnon oppitunnit ovat. Pätevien opettajien puute on suurin ongelma vähemmistöuskontojen osalta, vaikka luokanopettajien suhteen voi kysyä, onko kaikilla heistä kykyä tai halua pyrkiä opsin mukaiseen opetukseen enemmistökatsomusopetuksessakaan. En ole varma, saisiko esimerkiksi shiiamuslimi tai katolisen perheen nuori riittävän tuen oman katsomuksellisen identuteetin turvalliselle mutta kriittiselle rakentamiselle, jos suurimman osan katsomusopetuksesta hoitaa joka tapauksessa luokanopettaja, jonka omat katsomukselliset arvot saattavat näkyä läpi opetuksessa.

Yhteiselle katsomusopetukselle esitetään lakialoitteen perusteluissa keskenään osin yhteensopimattomia tavoitteita. Toisaalta kaivataan oman identiteetin rakentamiseen keskittyvää opetusta, toisaalta kantaaottamatonta täysin neutraalia tietoon perustuvaa opetusta. Kaivataan säästöjä - ja samaan aikaa dialogisuuden kehittymistä ja entistä parempaa ymmärrystä katsomusrajojen yli, samaan aikaan kun halutaan perustuslain hengessä häivyttää uskontokuntiin kuuluvuus ja kuulumattomuus näkyvistä. Moni varmaan tunnistaa riskiksi sen, että lapsi tai nuori joutuu edustamaan tiettyä ryhmää ja puolustamaan sen olemassaoloa sen sijaan että hänellä on aikaa ja tilaa tutkailla (myös kriittisesti) omaa suhdettaan siihen kulttuuriperintöön, johon hänen vanhempansa ovat kasvaneet tai jonka he ovat lapselleen valinneet.
Yhteisen katsomusaineen sisällöistä piirtyy kuva, jonka mukaan opetus keskittyy etiikkaan ja uskontotietoon, johon lisätään yhtenä katsomusvaihtoehtona uskonnottomuus, joka näyttäytyy tässä kontekstissa eniten jonkun puuuttumisena, ei monia mahdollisuuksia sisältävänä katsomusperheenä. Tämä on ainakin oma pelkoni. Yhteinen uskontotieto voi olla ihan mukavaa, mutta peruskoulun tasolla sitä kautta tuskin päästään kovin syvälle mihinkään uskontoon ja siten kaikki uskonnot näyttäytyvät helposti outojen tapojen ja uskomusten sekavana vyyhtinä. En usko, että nykyisiä resursseja pienentämällä päästään kovin helposti siihen, että uskontojakaan koskeva tieto muuttuisi suvaitsevaiseksi käyttäytymiseksi ja kulttuuritaidoksi tai että opiskelijoiden suhde oppiaineeseen muuttuisi myönteisemmäksi, koska katsomusaineet ovat opettajaherkkiä aineita ja koko opettajajoukkoa ei vaihdeta. Osalla luokanopettajia on voimakkaita mielipiteitä uskonnollisista kysymyksistä; tiedän tapauksia, joissa opettaja on käyttänyt uskontotunteja matematiikkaan koska ei ole keksinyt mihin saa kaksi viikkotuntia käytettyä, ja toisaalta Suomesta löytyy myös (kristittyjä mutta varmaan myös henkisiä tai muslimeja tai ateistisia) opettajia, joiden uskonnollinen/katsomuksellinen julistus ei pysy koulun ulkopuolella.

Hyviä puolia yhteisessä katsomusaineessa olisi se, että alakoulun uskonnon oppimateriaalit tulisi uudistaa suuntaan, jossa tehdään selkeämpi ero uskon ja tiedon välillä alusta asti. Uskonnonvapaus negatiivisessa mielessä toteutuisi myös paremmin, tosin käytännössä siitäkään ei ole takeita.

Nylyisen uskonnon ja katsomuksen opetuksen ongelmia on: osa opiskelijoista ei koe opetusta itselleen relevantiksi, valinnanvapautta ei kunnioiteta, eeteen ja vähemmistöuskontojen opetuksen järjestelyissä on puutteita, meissä opettajissakin on varmasti vikamme.

Veikkaan, että yhteisen katsomusaineen suuntaan kulkeminen jatkuu, vaikka naapurimaiden uskontotietomallista saatu kokemus kertoo, että katsomusaloitteen kannattajien mielikuva toteutuvasta opetuksesta ja sen tuloksista ei ehkä vastaa tosiasioita. Toivoisin kuitenkin malttia: opetussuunnitelmat on juuri uudistettu ja juuri dialogisuuden ja omakohtaisuuden lisäämiseen on panostettu.

Islamin opetuksen kehittäminen ja siihen satsaaminen olisi nyt tärkeää. Isis värvää juuri niitä nuoria, joiden käsitys omasta uskonnosta on haurain ja perustuu valtaväestön syrjiviin projektioihin.
Toinen kehittämistä vaativa alue olisi alakoulun katsomusopetus: sen tulee olla alusta asti yksilön omaa katsomusvapautta arvostavaa ja kunnioittavaa. Julkunen katsomusopetus ei myöskään saa olla ristiriidassa koulun tiedeopetuksen kanssa, muuten ollaan oudossa tilanteessa.

Komas kehitysehdotukseni on katsomusaineen valinnan vapauden avaaminen myös uskontokuntiin kuuluville lapsille ja nuorille. Tämä aiheuttaisi myös tervettä kilpailua lapsille ja nuorille relevanteista sisällöistä. Valinnanvapauden ei tarvitse olla tempoilevaa ja johtaa ennakoimattomuuteen, jos se toteutetaan kuten tähänkin asti. Suosituksena voisi olla, että muutoksen katsomusaineesta toiseen voi tehdä kerran kouluastetta kohden ja muutos on sitova. Rehtorille jäisi oikeus antaa luoa muutokseen perustellusta syystä tämänkin suosituksen ylitse.

Haluaisin silti joitakin muutoksia myös nykyisiin opseihin, mutta sen aika tulee seuraavassa opetussuunnitelmauudistuksessa. Toivoisin jokaiselle lapselle ja nuorelle eeteen keskustelevuutta ja mahdollisuutta pohtia myös uskontoihin liittymättömiä katsomuksellisia kysymyksiä kuten mediaa, vallankäyttöä, identiteettiä, ja hyvän uskonnonopetuksen tuottamaa yleissivistystä, kulttuurien lukutaitoa ja lähtökohtaisesti kunnioittavaa muttei kritiikitöntä suhdetta erilaisiin perinteisiin.