Accelerating Future

From The Independent:

Even by Silicon Valley standards, the grand design drawn up by William and Michael Andregg is hugely ambitious. Halcyon Molecular, the company that the brothers founded in 2008, is developing a way to sequence the human genome – and thus unlock the deepest secrets of DNA – faster and cheaper than ever before, and they have embarked on their adventure with financial muscle from billionaire members of a venture-capitalist fraternity known as the PayPal Mafia. That, on the face of it, sounds commendable enough, but there’s a two-part qualification to their basic plan which places the enterprise outside of the ordinary and teases the limits of the imagination.

First, there is the relative inexperience of the Andregg brothers. William is 29, Michael just a year older, and both are college drop-outs — but given Silicon Valley’s impressive track record for nurturing and funding obsessive, unconventional young innovators, their age is hardly unusual. The surprise is the long-term mission of Halcyon Molecular: to solve “the biggest challenge humans can individually face – disease and mortality”, as the mission-statement poster in their office reception says. Put another way, they’re supercharging the effort to map life’s biological code in almost unimaginable digital detail and, by doing so, ultimately, to attempt to conquer death itself.

I did a half-time stint for Halcyon Molecular last Fall, contributing to their website and other writing projects.

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Dennis Bray: What Cells Can Do That Robots Can’t from Singularity Institute on Vimeo.

Here’s the abstract.

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Ramez Naam: The Digital Biome from Singularity Institute on Vimeo.

Abstract:

Exponential technologies offer the promise not only of changing the human condition, but of radically altering the face of the planet on which we dwell. Within the next 20 years we will have sequenced the genome of every known species on the earth and tremendously advanced our understanding of how to utilize those genes and reprogram those organisms to alter the biosphere. Biosphere engineering will play a major role in overcoming current environmental and resource challenges, including finite reserves of fossil fuels and looming changes to the earth’s climate. That is just the beginning. An understanding of the complete biome genome will bring tremendous agility in combating future infectious disease outbreaks, in creating new sensors and manufacturing capabilities, and in revolutionizing food. Biosphere engineering and its underlying technologies will allow us to dramatically raise the population carrying capacity of the planet to tens of billions of individuals at least. With effective technology to sculpt the planetary biome, the limits of the number of humans that can live on the planet, and the quality of life of each, at tremendously higher than they appear to be today. This talk will explore some of the lower bounds of what’s possible with control of the biome.

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Brian Wang has an interview up with gene sequencing expert William Andregg. Here’s one good question answer:

Question: How do your views on longevity and life extension compare with those of Aubrey de Grey and Ray Kurzweil?

Answer: Parts of SENS urgently should be funded and tested. That being said, I work on sequencing and not on SENS, because our approach to curing aging is first to turn biology into an information science- actually getting to untangling the morass of metabolism that SENS does an end run around. I believe we can get to a complete mechanistic understanding of human biology in only a few decades, which is a timeline more like Kurzweil’s. On the other hand, if SENS were being vigorously pursued today, it might save millions of lives before the total understanding approach avails us. It is good to have multiple bets.

As for Kurzweil, maybe this isn’t fair, and I’d like to hear his thoughts on it, but I’m afraid his books demotivate people who would otherwise contribute to the cause, maybe by giving the impression to some that the Singularity is not only coming, but actually inevitable. Eat right, exercise, take these pills, and don’t worry- those smart hardworking scientists over there will solve everything for you. In contrast, a great thing about Aubrey as a leader is that he harangues people to actually get off their asses and make a contribution.

We might not survive the next twenty years. We may never cure aging. There is nothing inevitable about our success. Everyone who is talented enough to make a contribution should be trying to help, on all fronts, by any ethical means, like it’s life and death – because it is.

And the very most talented ones should send their resumes immediately to Halcyon.

I definitely agree that there is “nothing inevitable about our success”. An accidental or purposeful nuclear war could more or less destroy our civilization at any time. You could be hit by a bus tomorrow. The laws of physics are neutral to human affairs. The universe is not our daddy that loves us. It’s merely a game board on which atoms bump into each other, and in a tiny corner of that game board happen to be some monkeys that love fighting, and like to build all sorts of fun toys to keep fighting.

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Do you excel in any of the following areas?

• Electrical Engineering
• Mechanical Engineering
• Image Analysis
• Thin Film Deposition
• Business Operations
• Electron Microscopy
• Systems Integration
• Materials Science
• MEMS
• Applied Physics
• Computer Science
• Automation / Robotics
• Organometallic Chemistry
• Microfluidics
• Optics

More details on necessary skills is available here.

If so, and you’re interested in working for the most exciting biotech startup in California and possibly even the world, I encourage you to send me your resume and a short letter describing your skills and interests. You can learn more about Halcyon Molecular at the website, updates, and technology pages.

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You can find it here.

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PhysOrg:

(PhysOrg.com) — Biomedical researchers at the University at Buffalo have engineered adult stem cells that scientists can grow continuously in culture, a discovery that could speed development of cost-effective treatments for diseases including heart disease, diabetes, immune disorders and neurodegenerative diseases.

UB scientists created the new cell lines – named “MSC Universal” – by genetically altering mesenchymal stem cells, which are found in bone marrow and can differentiate into cell types including bone, cartilage, muscle, fat, and beta-pancreatic islet cells.

The researchers say the breakthrough overcomes a frustrating barrier to progress in the field of regenerative medicine: The difficulty of growing adult stem cells for clinical applications.

Because mesenchymal stem cells have a limited life span in laboratory cultures, scientists and doctors who use the cells in research and treatments must continuously obtain fresh samples from bone marrow donors, a process both expensive and time-consuming. In addition, mesenchymal stem cells from different donors can vary in performance.

The cells that UB researchers modified show no signs of aging in culture, but otherwise appear to function as regular mesenchymal stem cells do – including by conferring therapeutic benefits in an animal study of heart disease. Despite their propensity to proliferate in the laboratory, MSC-Universal cells did not form tumors in animal testing.

Fantastic.

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In the comments, Martin said:

I wonder how accurate it is. Uncle Fester became underground famous in the 90s when he published books on meth and acid manufacture, but other clandestine chemists criticized his syntheses for being inaccurate.

From this small snippet, it sounds like he wants you to go out and find the right Clostridium species and strains in soil and culture them yourself, which sounds as impractical as his suggestion in the acid book to grow acres of ergot-infested rye. :)

Any more comments on why this is impractical? It sounds much simpler than growing acres of ergot-infested rye. He describes how he would isolate spores, first by heating the culture (this kills anything that is not a spore), then encouraging growth in an anoxic environment (kills anything that is not anaerobic). This leaves only anaerobic bacteria derived from spores.

The book does claim that botulinum germs are “fussy about what they like to grow in, its pH, and its temperature” and that “This need to exclude air from the environment where the germs are growing is the most difficult engineering challenge to the aspiring cultivator of Clostridia botulinum“, so he’s not saying that it’s a cakewalk.

Of course, many of these underground books (Anarchist Cookbook…) are rife with misinformation. Anyone serious about producing botulism toxin would need actual biochemical knowledge and multiple corroborating sources. Still, there’s a lot of information in this particular book that would at least provide a compelling starting point.

It’s worth noting that Uncle Fester probably never synthesized all the compounds described in his book, which includes over half a dozen different types of nerve gas. He repeatedly points out that synthesizing these chemicals is a risk to the life of the person performing the synthesis. In some parts of the book, he names sources, like literature released by the military, but the vast majority of his book lacks citations.

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A minor personal announcement — I’ve been hired to work half-time for Halcyon Molecular in Redwood City. I’m mostly going to be working on improving their website content. Halcyon was founded by Michael and William Andregg, who I originally met in Tucson at a Center for Responsible Nanotechnology conference in 2007.

Halcyon is developing a technology to sequence genetic material at orders of magnitude faster than anything on the market or in the pipeline. Their technology and approach, which uses electron microscopy, is really unique. I’m happy I finally get to talk about the company and technology a bit in public because I’ve been excited about them in private for a long time.

You can read more about Halcyon at their website or at this TechCrunch article.

Also keep in mind that Halcyon is actively looking for new researchers.

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From The Wall Street Journal:

Rapid advances in bioscience are raising alarms among terrorism experts that amateur scientists will soon be able to gin up deadly pathogens for nefarious uses.

Fears of bioterror have been on the rise since the Sept. 11, 2001, attacks, stoking tens of billions of dollars of government spending on defenses, and the White House and Congress continue to push for new measures.

But the fear of a mass-casualty terrorist attack using bioweapons has always been tempered by a single fact: Of the scores of plots uncovered during the past decade, none have featured biological weapons. Indeed, many experts doubt terrorists even have the technical capability to acquire and weaponize deadly bugs.

The new fear, though, is that scientific advances that enable amateur scientists to carry out once-exotic experiments, such as DNA cloning, could be put to criminal use. Many well-known figures are sounding the alarm over the revolution in biological science, which amounts to a proliferation of know-how—if not the actual pathogens.

Another bit later in the article:

All the government attention comes despite the absence of known terrorist plots involving biological weapons. According to U.S. counterterrorism officials, al Qaeda last actively tried to work with bioweapons—specifically anthrax—before the 2001 invasion of that uprooted its leadership from Afghanistan.

This is great. It’s best to pay attention to obvious risks, like this, nuclear terrorism, the integrity of the power grid under solar storms, major earthquakes, etc., before they happen, not after. Often times, adequate preparation even requires little marginal effort.

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Ecology: A world without mosquitoes.

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From Eurekalert:

Gladstone scientists discover new method for regenerating heart muscle by direct reprogramming

Next-generation reprogramming of native cells offers therapeutic advantages

Scientists at the Gladstone Institute of Cardiovascular Disease (GICD) have found a new way to make beating heart cells from the body’s own cells that could help regenerate damaged hearts. Over 5 million Americans suffer from heart failure because the heart has virtually no ability to repair itself after a heart attack. Only 2,000 hearts become available for heart transplant annually in the United States, leaving limited therapeutic options for the remaining millions. In research published in the current issue of Cell, scientists in the laboratory of GICD director Deepak Srivastava, MD, directly reprogrammed structural cells called fibroblasts in the heart to become beating heart cells called cardiomyocytes. In doing so, they also found the first evidence that unrelated adult cells can be reprogrammed from one cell type to another without having to go all the way back to a stem cell state.

The researchers, led by Masaki Ieda, MD, PhD, started off with 14 genetic factors important for formation of the heart and found that together they could reprogram fibroblasts into cardiomyocyte-like cells. Remarkably, a combination of just three of the factors (Gata4, Mef2c, and Tbx5) was enough to efficiently convert fibroblasts into cells that could beat like cardiomyocytes and turned on most of the same genes expressed in cardiomyocytes. When transplanted into mouse hearts 1 day after the three factors were introduced, fibroblasts turned into cardiomyocyte-like cells within the beating heart.

“Scientists have tried for 20 years to convert nonmuscle cells into heart muscle, but it turns out we just needed the right combination of genes at the right dose,” said Dr. Ieda.

Continue.

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