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Koene R.A.,Halcyon Molecular
International Journal of Machine Consciousness | Year: 2012

Whole brain emulation aims to re-implement functions of a mind in another computational substrate with the precision needed to predict the natural development of active states in as much as the influence of random processes allows. Furthermore, brain emulation does not present a possible model of a function, but rather presents the actual implementation of that function, based on the details of the circuitry of a specific brain. We introduce a notation for the representations of mind state, mind transition functions and transition update functions, for which elements and their relations must be quantified in accordance with measurements in the biological substrate. To discover the limits of significance in terms of the temporal and spatial resolution of measurements, we point out the importance of brain region and task specific constraints, as well as the importance of in-vivo measurements. We summarize further problems that need to be addressed. © 2012 World Scientific Publishing Company.


Koene R.A.,Halcyon Molecular
International Journal of Machine Consciousness | Year: 2012

Whole brain emulation aims to re-implement functions of a mind in another computational substrate by carefully emulating the function of fundamental components, and by copying the connectivity between those components. The precision with which this is done must enable prediction of the natural development of active states. To accomplish this, in vivo measurements at large scale and high resolution are critically important. We propose a set of requirements for these empirical measurements. We then outline general methods leading to acquisition of a structural and functional connectome, and to the characterization of responses at large scale and high resolution. Finally, we describe two new project developments that tackle the problem of functional recording in vivo, namely the "molecular ticker-tape" and the integrated-circuit "Cyborcell". © 2012 World Scientific Publishing Company.


Patent
Halcyon Molecular | Date: 2011-11-22

A scanning transmission electron microscope includes an electron beam source to generate an electron beam. Beam optics are provided to converge the electron beam to a probe, such as a longitudinally stretched probe. A stage is provided to hold a specimen in the path of the electron beam. The specimen comprises one or more polymers to be sequenced. A beam scanner scans the electron beam across the specimen. A controller may define one or more scanning areas corresponding to the locations of the polymers, and control one or more of the beam scanner and stage to selectively scan the electron beam probe in the scanning areas. The controller may also tune the beam optics during imaging. One or more detectors are provided to detect electrons transmitted through the specimen to generate an image for each of the scanning areas. The controller may also analyze the one or more images to sequence the polymers.


Patent
Halcyon Molecular | Date: 2011-02-10

A transmission electron microscope includes an electron beam source to generate an electron beam. Beam optics are provided to converge the electron beam. An aberration corrector corrects the electron beam for at least a spherical aberration. A specimen holder is provided to hold a specimen in the path of the electron beam. A detector is used to detect the electron beam transmitted through the specimen. The transmission electron microscope operates in a dark-field mode in which a zero beam of the electron beam is not detected. The microscope may also be capable of operating in an incoherent illumination mode.


Patent
Halcyon Molecular | Date: 2011-06-07

A transmission electron microscope includes an electron beam source to generate an electron beam. Beam optics are provided to converge the electron beam. An aberration corrector corrects the electron beam for at least a spherical aberration. A specimen holder is provided to hold a specimen in the path of the electron beam. A detector is used to detect the electron beam transmitted through the specimen. The transmission electron microscope may operate in an incoherent mode and may be used to locate a sequence of objects on a molecule.


This week’s episode of Speaking Of… (video below) features the founder/CEO of Halcyon Molecular, William Andregg. Andregg grew up in Arizona. There’s a song by The Orb called Little Fluffy Clouds that describes the light-pollution-free Arizonan sky quite perfectly, with amazing clouds, sunsets and stars. Most Arizonans – at some point in their lives – will lay on the hood of their car and gaze towards the grandness of those fluffy clouds and the Milky Way, but most probably won’t come to the same conclusions that William did about it all. William yearned to travel beyond the clouds to the stars, but become perplexed by the fact that he most likely wouldn’t make it due to an unfortunate condition that plagues us all — mortality. He knew that in order to reach the stars, which he so desperately wanted to do, he must dedicate most of his life to prolonging and increasing human lifespans so that he or others like him might have a chance to go where no man has truly gone before. In order to go big, he went very small. Our DNA. Halcyon Molecular has come out of stealth mode, letting William tell his story in order to encourage a few good business women and men to join their plight to end aging. They’ve discovered an inexpensive and most importantly, fast way to sequence the entire human genome. If commercialized successfully, their discovery will change the world of medicine as we know it and increase our chances of living even longer. Biotech startups are rare now, but we’re going to start seeing more and more of them pop up over the next decade. Technology that was once incredibly expensive is now becoming obtainable and the next wave of tech startups will delve into the largest market of all, human health. William is the only person I know with one of the world’s most powerful electron microscopes operating out of his garage, which is pretty damn cool. What about frogs? Well, the dissection of frogs in high school almost led to William avoiding an entire career in biotech, which struck me as one of many things we should consider revising in our public education system. We need more Williams, not fewer.


News Article | August 20, 2012
Site: gigaom.com

Halcyon Molecular, a much-talked about genetics startup that was started by Andregg Brothers – William and Michael in 2008 has quietly gone away. It is not clear if the company has shut down – the web site exists – but sources familiar with the Redwood City, Calif.-based company say that it ran out of money. Its investors included Peter Thiel’s Founder’s Fund and maverick investor/entrepreneur Elon Musk. In its life, the company had snagged upwards of $20 million in funding. I am awaiting comment from Founders Found and Musk. It is a bit of a bummer since I always root for such startups whose foundation is pure technology and whose ambition to change the future. In 2009, when Founders Fund partner Luke Nosek joined Halcyon, in an email he noted that the company would one day it would be able to “sequence 100 percent complete human genome in less than ten minutes for less that $100.” Earlier this year Oxford Nanopore team had beaten Halcyon to the punch. It was one of the companies that was working on low cost DNA sequencing technologies and it is one of the reasons why I kept tabs on the company. The company listing recently went missing on the Founders Found website. Here is an article from The Independent from last year that highlights company’s plans and ambitions – it is worth reading.


News Article | March 17, 2015
Site: www.fiercebiotech.com

Investment guru and self-described contrarian Peter Thiel is best known for making a bundle from PayPal and Facebook. But along the way he's made a few small bets on biotech, and MIT's Technology Review caught up with him recently to find out more about what is driving his interest in the field, and what he looks for when he invests in a biotech. "Most companies are very heavily invested in the unpredictably paradigm," he tells the magazine. "But when you treat it as a lottery ticket, both the participants and the investors have already psyched themselves into losing. A small probability times a big payoff normally equals zero." But the author of Zero to One (the title relates to making vertical vs. horizontal progress) is also not too fond of the me-too strategy, where everybody is piling into the same field. "I would say everything that fits a trend is bad, just always bad," he says. Thiel keeps the biotech fires burning on two fronts, through his charitable Thiel Foundation--which created Breakout Labs--as well as his venture arm, Founders Fund, which has invested in Cambrian, Emerald Therapeutics, and the antibody play Stem CentRx. One of his investments, a company called Halcyon Molecular that set out to device a cheap approach to sequencing, failed. The foundation has been backing projects involved in translational research, taking academic projects and pushing a product to the market. And the venture investor only wants companies that are directed by the founders. There's something else that drives Thiel's interest. He talks to Technology Review about his interest in anti-aging programs, something that spurred him to take growth hormones and sign up for cryonic freezing. "The way people deal with aging is a combination of acceptance and denial," he says. "They accept there is nothing they can do about it, and deny it's going to happen to them. - here's the link to the story Related Articles: Billionaire Thiel backs biotech startups with eyes on Alzheimer's, GI disease Tech billionaire Thiel raises $1B for fifth venture fund Thiel's Breakout Labs awards new grants to biotech startups


News Article | July 13, 2011
Site: thenextweb.com

As a Brit who gave up cheerleading the European tech scene to make the pilgrimage to Silicon Valley to live, eat and breath the world’s leading hub for technology startup innovation, I’ve been largely unimpressed and disappointed by the quality of startups here. Living in San Francisco since January, I’ve interviewed around two hundred startups and there’s only two, out of two hundred, I think are game changers. Now, don’t get me wrong, Silicon Valley is an incredibly inspiring place to be. Everyone is doing something amazing and trying to change the world, but in reality much of the technology being built here is not changing the world at all, it’s short-sighted and designed for scalability, big exits and big profits. Groupon clone after Groupon clone, yawn… yet another social media dashboard, a cloud-based enterprise solution or, worse still, another photo sharing app; I’ve heard pitch after pitch of the same technology and keep wondering why all these highly intelligent, well educated youngsters, many of whom have been educated in the best universities in the world (Stanford, Yale and Harvard) are not putting their brains to good use by solving real-world problems. Instead they’re building technology to solve trivial issues – like apps that show where to spot your nearest tofu cupcake and share it with your friends. I’ve come to the conclusion that entrepreneurship in the Valley has become productized, as organizations like Y Combinator attempt to marginalize, commoditize or manufacture a process that is inherently risky. The YC model of startups gaining $150,000 upon entering the accelerator program means investor Yuri Milner and the rest of the Start Fund venture capitalists’ get a nice stake in every company that goes through the program. The problem is that it’s all about the money; it creates emphasis on Y Combinator startups to quickly exit or IPO. At a BBQ last week with a group of Y Combinator graduates, the conversation went predictably back and forth, sounding something like this: What batch were you in? How many times did you pivot? How much did you raise? From who? How many users have you got now? What’s your growth rate? Who’s going to acquire you? It’s never about the technology or impact it’s having, it’s about the game of entrepreneurship; getting users, funding and exiting as quickly as you can. From an investor’s perspective, it’s a clever model; you put a group of extremely talented and hard working graduates together, give them seed funding, keep them lean and they pivot until they get you a hit and you make your return. But I wonder if the model is counter productive, producing risk averse entrepreneurs who, if they follow the right procedure, are almost guaranteed success in the form of a talent acquisition or exit. Should this be what entrepreneurship is about? What happened to irreverence, thinking outside the box, wanting to make a difference in the long run? As much as I moan, Y Combinator is producing some game changers – Airbnb is one of them, not for what they are now but for founder Brian Chesky’s vision to become the eBay for traded goods. If it works it could put a halt on manufacturing new goods and put a stop to the raping of Earth’s limited resources. Udemy is another favourite; they are democratizing education by cutting out the institution and helping people learn in a structured way that goes deeper than Googling a query, giving anyone with a smartphone access to a Stanford level of education. But for every Airbnb and Udemy there are always more Netflix, Evernote and Spotify clones. VC Brian Singerman, Principal at Founders Fund, confirmed my thoughts about the gold-rush mentality. ‘Many entrepreneurs are in it for the wrong reasons, they should be more focused on doing something big and good for the world and figuring where the money comes after that.’ We both agreed there was an abundance of trivial tech in the Valley, but also that there is innovation happening around health care related startups, so I rushed to show him a startup I interviewed recently – one of the few startups I thought had legs – only for him to tell me he’d just invested in the company, which led us into talking about the VC landscape where some VCs are buying a lottery ticket, investing in startups to get rich quick. It was refreshing to hear Brian share my thoughts and hear that he puts his fund to good use: “I invest in anything involving a biology and technology that does not require clinical trials or hundreds of millions of capital,” he said, pointing to his Halcyon Molecular tee shirt – a DNA sequencing company that he’d recently invested in. One of the reasons for lack of innovation in the Valley is that entrepreneurs are not exposed to enough real-world problems. It’s all relative of course, but the problems facing well-educated young people in San Francisco are certainly different from that of entrepreneurs in emerging markets. I can’t blame the entrepreneur too much though, I suppose it’s the traditional model of supply and demand; consumers in the USA clearly want to play Angry Birds, whereas in some African countries consumers are more likely to be searching for their nearest Malaria drugs clinic. Every government in the world is trying to recreate what is going on in the Valley as they see it as a way out of the global recession and into job creation. Tech hubs are springing up all over the world in places you wouldn’t even imagine. Combine that with the fact that many entrepreneurs can’t get to the US because of visa issues (the Startup Visa Act could take another couple of years before it passes through both the House and the Senate) and you’ve got a recipe for startups that are solving real world-problems, outside of Silicon Valley. There are also other incentives for entrepreneurs to build outside of the valley; Startup Chile is a government-backed organization that is encouraging entrepreneurs to build startups with the enticement of cheap developers – a scarcity in the Valley. Kundavi is building a community in Cabo, Mexico for startups, which not only has the promise of cheap cost of living for the bootstrapped entrepreneur, but is also geographically on a similar time zone (one hour later) with Silicon Valley, which makes phone calls with investors easy. There is one thing though, that continues to set Silicon Valley apart from every other technology hub on the planet and that’s access to finance. The funding ecosystem here is unlike any other in the world. The European tech community has come a long way since I came onto the scene in 2008 with three or four tech events every night, but in terms of funding it does not even begin to compete with Silicon Valley. But the funding landscape is changing due to the cost of innovation decreasing rapidly which means anyone with a laptop and a WiFi connection can get an idea off the ground for dirt cheap. Valley VCs are noticing this global trend and getting smart with it – angel investor Chris Sacca is investing in European startups; Dave McClure evangelizes his 500 Startups accelerator around the world with Geeks on a Plane, and Paul Bragiel’s i/O ventures is now one of the leading investors in East Africa. Journalist Sarah Lacy’s latest book reports on how entrepreneurs from emerging markets are taking local chaos and turmoil and turning it into opportunities, making millions and creating thousands of jobs – Valley entrepreneurs should take note of these self starters who through adversity are taking massive risks and succeeding. If Silicon Valley wants to keep its number one spot as global startup innovator both entrepreneurs and VC’s need to get out of the bubble and go and see real problems in the world so they can start innovating and driving change. Obama needs to quickly pass the Startup Visa Act into US law, more media should cover tech outside the Valley, and this San Francisco fog better go away quickly – or I’m moving to Cabo.

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