Halcyon Molecular: whole genome sequencing well under $1000?

Halcyon Molecular is a quite ambitious startup,  don’t you think?

What we do:
Halcyon Molecular is developing an ultra-low-cost DNA sequencing technology. Our single molecule approach does not require PCR amplification and will allow for megabase read lengths with simultaneous determination of methylation pattern. We aim to sequence entire human genomes de novo for well under the “holy grail” cost-to-consumer of $1000.

Going to LA to end aging for 3 days & maybe more

It is just good to go to a conference where the overwhelming majority of attendees think (and many of them act) that by science & technology we can actually get rid of aging related health problems and develop a robust life extension technology. I sense a lot of freedom here which I sense since the age 15 but now – thanks to Aubrey de Grey – this is all happening in a community (with a diverse chronological age distribution) that is becoming more established and more funded. Whether this is only a freedom to do something or also a freedom from a constraint or from interference… well you are free to decide it dear readers.

The “Understanding Aging: Biomedical and Bioengineering Approaches” conference will be held from June 27-29, 2008 at UCLA organized by Aubrey de Grey, Irina Conboy and Amy Wagers.

The emphasis this time (just check the coorganizers Conboy and Wagers) is on stem cell research and regenerative medicine, which I think is the only coherent engineering concept outside for robust life extension in the form of systemic regenerative medicine while SENS by definition (strategies) is a flexible enough umbrella term to include other coming life extension technologies and concepts under its brand.

In the age of Twitter and FriendFeed the blog genre is just too slow to cover the event, so I use the FriendFeed room for the conference as it seems to be a perfect place of live microblogging the conference, sharing any kind of links, videos, comments, feeds and feedbacks. I hope others will make it too.

Alexis writes on Wired: Continue reading

Petabyte Age Wiredesque lesson on what science can learn from Google

I argued many times here that biology based biotechnology is the next information technology but in order to do so, biotech should harness good IT patterns and mimic its massive computing practices to handle the enormous amount of constantly accumulating data. Often this trend could be summarized in a simple way: keep your eye on Google and conduct thought experiments in advance in which science is done in a Googleplex like environment in terms of the computing & financial resources and algorithm heavy engineering culture. Use Python and learn cluster computing and MapReduce. With the expected launch of the massive scientific dataset hosting Google service – nicknamed Palimpsest – this year finally a direct interface between scientists and Googlers emerges and hopefully opens up possibilities for scientists to cooperate with Google. (Remember my joke on Google BioLabs back in 2006)? I get emails from biologists, bioinformaticians asking me how to be hired by Google ever since then. As I tweeted yesterday: I growingly have the impression that “being ambitious” today = ‘worked, is currently working, is going to work at/for Google’ Taking Google’s inter-industrial power into consideration I see a real chance that some day the “Google of Biotechnology” title goes not to a startup yet to be emerged, not to Genentech or to 23andMe but……to Google itself. No kidding here. Fortunately Google’s model is “to build a killer app then monetize it later” says Andy Rubin, the man behind Google’s Android mobile software in the July issue of Wired so scientists working for the big G probably won’t have to worry about turning their scientific killer app into an instant cash machine.

And now in the very issue of Wired magazine (not online yet ) there is an exciting cover story on the same pattern I talked about concerning the life sciences but in the broader context of every kind of science with the provocative, Fukuyama-like title The End of Science. There is a witty and short essay from editor-in-chief Chris Anderson entitled The End of Theory followed by examples of the ‘new science’ like the The Large Hadron Collider expected to generate 10 petabytes if data/second, The Sloan Digital Sky Survey heaven catalog maker accumulating 25 terrabytes of data so far, the skeleton scanning project of Sharmila Majumdar and the Many Eyes project “where users can share their own dynamic, interactive representations of big data”.

For many people around the globe, Chris Anderson is a freeconomist & the author of a popular airport book but fewer people are aware that he was actually trained as a (quantum) physicist and even worked at Los Alamos Continue reading

Compare scientific websites with a new Google Trends layer!

I always had the feeling that the Natureplex (the web division of the Nature Publishing Group headed by Timo Hannay) is ahead of most scientific journal publishing conglomerate’s similar departments. Now with the help of a new Google Trends layer that compares websites in terms of traffic this impression was confirmed again without strict numbers. I hope that more and more scientific journals gain incentives finally to experiment with new web technologies. Also a quick look to the Regions comparison on the bottom left helps you give up the history based conclusion that Science is the number 1 on the web in the US compared to Nature while Nature is so UK and Europe centric.

“Today, we add a new layer to Trends with Google Trends for Websites, a fun tool that gives you a view of how popular your favorite websites are, including your own! It also compares and ranks site visitation across geographies, and related websites and searches”

Source: Official Google Webmaster Central Blog via Webmonkey

The same comparison with Alexa: Continue reading

UCSF Memory & Aging Center channel on YouTube & ‘Fight for Mike’

Even tech people in Silicon Valley need to join their powerful forces and sources when it is about aging related neurodegenerative diseases and help research and the clinic.

UCSF Memory and Aging Center channel on YouTube 

Om Malik: A Personal Note: Pause & Read via John Battelle

 

Innovation stop: “All they’ve done is created an extra billing event for the doctor”

It’s my first real encounter with a situation in which the officials of the state of California are clearly against innovation for financial reasons obvious enough (is enough):

Wired Science, Alexis Madrigal, upcoming BioBarCamper:

Exclusive: DNA Tester Reveals Cease-and-Desist Letter

Wired.com has obtained a copy of the cease-and-desist letter sent to Navigenics by the state of California’s Public Health Department from a company spokesperson.

The letter’s strongest wording is reserved for another section of the law, Business and Professions Code Section 1288, which requires a doctor’s note for all laboratory tests, unless, like pregnancy tests, they are exempt from that law.

“Genetic tests are NOT exempt,” the letter reads. “As such, the test must be ordered by a physician or surgeon.” Continue reading

Future stop: California health officials against personal genetics risk-takers

It’s official: The California Department of Public Health wants practicing physicians (many of them prehistorically, sorry, traditionally trained) to be the patres familias in issues between personal genetic test takers and direct-to-consumer personal genetic testing start-ups while declining the test takers’ right to get familiar with their own genetic makeup and risks by their own.
Calif. cracks down on 13 genetic testing startups

California health regulators have demanded that 13 direct-to-consumer genetic testing startups halt sales in the state until they prove they meet state standards. All the companies have two weeks to demonstrate to regulators that their laboratories are certified by the state and federal governments, said department spokeswoman Lea Brooks. The startups also must show the tests they are selling California residents have been ordered by a doctor as required by state law.

I give you trusted links instead of complicating your day with my own opinion: Continue reading

Understanding Aging Conference on FriendFeed!

The “Understanding Aging: Biomedical and Bioengineering Approaches” conference will be held from June 27-29, 2008 at UCLA organized by Aubrey de Grey, Irina Conboy and Amy Wagers. I like to call it UndertsEnding Aging in myself and I am excited to go to LA and meet new people also people from SENS3.

Yesterday I created a FriendFeed room for the conference as it seems to be a perfect place of live microblogging the conference, sharing any kind of links, videos, comments, feeds and feedbacks. Working on aging and the postponement of it (you can bravely say life extension) is always a pioneering work so it’s time to use pioneering web apps for that purpose, just like FriendFeed.

Aubrey de Grey, Kevin Perrott and Kevin Dewalt have already joined the room. What about you? See you on FriendFeed, see you on LA!

Patent Board science strength of biotech firms in WSJ

The Wall Street Journal Patent Board Biotechnology Scorecard was published this week in which biotech companies & private research firms are grouped by their Patent Board science strength ranking “which is based on the scale, quality, impact, and nearness to core science of a company’s patent-based intellectual property”.

What I found interesting at the first sight is Geron‘s nice position and the lack of Genentech. Also take a look on the charts and compare, say Illumina and Affymetrix or the research intensity/innovation cycle ratio in case of the same company.

Says my source, San Diego biased marketing expert Rick Cook in an in medias res email:

“Three of the top 10 science-based researchers, according to the rankings, are based in San Diego. Several other San Diego companies fall outside the top 10.
Nanogen, one of my clients, made the rankings. What’s particularly interesting about Nanogen — who competes against #1-ranked Roche — is that the company has by far the lowest market cap (just over $28 million) represented in the rankings. In fact, if you divide patents issued by market cap, which could be used as a proxy for size, Nanogen ranks number one — dollar-for-dollar the most innovative company on the list.”

Help Craig Newmark find a new hobby on Twitter!

Internet celebrities are not celebrities in a sense that you can easily communicate with them on services like Twitter (assuming the services are not down). There’s no such thing as an internet bodyguard except some firewalls in Windows. So this day I found Craig Newmark, Craigslist founder tweeting this:

I suggested him a forward looking hobby:

To my surprise I got an the following answer back: Continue reading

80 is the new 50 so Carl Icahn has a blog without content.

Billionaire investor Carl Icahn (72) recently made the bloglines with his energetic position on the Microsoft – Yahoo deal. He has a blog too or at least it is coming soon since 01/31. /Having a blog for more than 3 months without any content is kinda equivalent with planning to sign up for Twitter but actually not doing it./

Daniel Gross, Newsweek: Eighty Is the New Fifty

“Carl Icahn has a blog (though it doesn’t contain any content)”….

“In time, it’s likely that prejudices toward older workers will be eroded less by the exploits of eternally youthful financiers, and more from a longstanding demographic trend. As they’ve moved through life, the baby boomers have altered societal attitudes on everything from smoking marijuana to Botox. As boomers coast into their golden years, it’s likely the acceptance of older workers at every rung of the corporate ladder will grow. In the 1960s, the boomers’ mantra was: don’t trust anyone over 30. In the 2010s, it’ll probably be: don’t trust anyone under 70.”

The Biogerontology Research Foundation receives charitable status, UK

Just landed in my mailbox, emphasis added by me:

Dear Attila,

I would like to provide you with a copy of the press release to be distributed via press release distribution sites on Wednesday. We will also put it on our site within a few hours after this email so you can confirm its authenticity. Please help us distribute this press release.

The Biogerontology Research Foundation, which has been started with the help of worlds’ most prominent scientists and businessmen received the charitable status from the Charity Commission for England and Wales.

The fact, which is not mentioned in the press release is that the chief scientific officer of the foundation is Dr. Michael Rose of UCI, who is famous for extending life of fruit flies threefold. Continue reading

The Sergey, Larry, Eric test by Anne & Linda: 23andMe at home

“We really think that we can change Health Care…I want to change it in 5 years…it has to change and that’s we all are about” – says Anne Wojcicki, 23andMe co-founder, in the Google Tech Talk on Googling the Googlers’ DNA: A Demonstration of the 23andMe Personal Genome Service.

Also a good presentation by Linda Avey, other co-founder, for instance on data privacy and service security: “We take the security of our customers’ data to the highest degree…you guys (Googlers) are very much of the same mind..One of our leading engineers is probably the most paranoid man we’ve ever meet and he is the perfect guy for that.

Here are my screenshots on the genetic puzzle on the Google triumvirate presented by Anne Wojcicki:

Continue reading

BioBarCamp: August 6-7, The Institute for the Future, Palo Alto

When I wrote about BioBarCamp for the first time, it was just an idea to organize an unconference for biogeeks, people interested in life scientists around SciFoo Camp time.

Now thanks to Alex Soojung-Kim Pang, Science X2 project leader, we have a date and a venue: August 6-7, The Institute for the Future, 124 University Avenue, Palo Alto, California 94301.

Capacity: around 100 people and we already have 15 signed up.

Sign up here (first-come, first-served)

Join the discussion, suggest topics/sessions or follow the wiki.

What path would you follow: Shumway or Barnard?

Monya Baker has an excellent Q&A with the authors of the recent Nature Insight: Regenerative Medicine over at The Niche blog. Ken Chien, the author of Regenerative medicine and human models of human disease – see earlier postrecalls the paradigmatic story of heart transplantation and the 2 main surgeons behind, Norman Shumway and Christiaan Barnard, who are perfect representatives of the different paths of pioneering clinicians:

Sometimes in looking forward it’s good to look back. In cardiac regenerative medicine, probably the only clear success to date is heart transplantation. From the initial grant that Norman Shumway received in 1958 [to study the possibility of heart transplantation] it took more than two decades before the procedure became routine.

Shumway was a careful, thoughtful man. He not only didn’t do the first heart transplant; he didn’t do the second. He was slowed down in the United States because of the regulatory barriers and ethical concerns. Christiaan Barnard, on the other hand, went back to South Africa and decided to just go for it. Sounds familiar?

We realized very quickly that this was not working, that the science was not there. In 1968, a year after his first attempt, Barnard gave up on the procedure and considered it a failure. Everyone gave up, except Shumway. He went back to the lab and spent the next ten years figuring it out. He realized that the issue was rejection. Continue reading

Synthetic morphology: what kind of animal is that?

As far as I understand synthetic morphology = develompental biology +synthetic biology + tissue engineering + anatomy to create new cellular patterns.

Jamie A. Davies: Synthetic morphology: prospects for engineered, self-constructing anatomies

“This paper outlines prospects for applying the emerging techniques of synthetic biology to the field of anatomy, with the aim of programming cells to organize themselves into specific, novel arrangements, structures and tissues. There are two main reasons why developing this hybrid discipline – synthetic morphology – would be useful. The first is that having a way to engineer self-constructing assemblies of cells would provide a powerful means of tissue engineering for clinical use in surgery and regenerative medicine. The second is that construction of simple novel systems according to theories of morphogenesis gained from study of real embryos will provide a means of testing those theories rigorously, something that is very difficult to do by manipulation of complex embryos. This paper sets out the engineering requirements for synthetic morphology, which include the development of a library of sensor modules, regulatory modules and effector modules that can be connected functionally within cells. A substantial number of sensor and regulatory modules already exist and this paper argues that some potential effector modules have already been identified. The necessary library may therefore be within reach. The paper ends by suggesting a set of challenges, ranging from simple to complex, the achievement of which would provide valuable proofs of concept.”

Maybe more light could be shed on the topic by comparison to regenerative medicine: Continue reading

23andWe follows 23andMe: First generation of Consumer-Enabled Research

Consumer-Enabled Research, the second goal of pioneering personalized genetics company 23andMe, reached its first generation with the launch of 23andWe.

From BusinessWire:

“23andWe marks a new approach to genetics research. By directly involving 23andMe customers in the company’s research projects, the goal is to conduct large-scale studies powered by a web-based community of diverse individuals who are willing to share information (on a confidential basis) about their health and other personal traits.”

video via Deepak

As Esther Dyson’s said on The Spittoon blog, which is the corporate blog of 23andMe: What You Can Do for 23andMe (and Future Generations) Continue reading

Problem: embryonic stem cell lines vary & iPS lines too

Finally I started to digest all the articles (usually on the streetcar on my way to work and home) from the recent Nature Insight: Regenerative Medicine and I try to pick up some stories for you (& interesting enough for me) from that, in case you are not lucky enough to have an available copy.

For clinicians, the lack of gold standard embryonic stem cell lines with the measurably same regeneration potential will be a huge technological problem later while this variability is an interesting basic science problem today.

Kenneth R. Chien: Regenerative medicine and human models of human disease

A central challenge to the development of human stem-cell-based models of disease lies in the need to isolate and expand rare cell populations reproducibly and then to fully differentiate enough of the cells of interest. In this regard, one of the main obstacles to establishing human ES-cell-based models is that ES cell lines vary. All lines do not have the same potential to differentiate into cells of a particular lineage, most probably as a result of inherent epigenetic, genetic and developmental differences at the time of their isolation. For example, a study of 17 independent human ES cell lines showed that 7 of these lines had little or no capacity to enter the cardiovascular lineage, and the level of cardiovascular markers expressed by 2 of the 17 cell lines was an order of magnitude or more higher than that of these 7 lines. Similar variability between human ES cell lines was observed for entry to the pancreatic lineage, and cell lines that were optimal for generating cells of endodermal lineages were extremely poor for generating mesodermal lineage cells in many cases. Thus, new human ES cell lines that are optimal for generating specific lineages of interest need to be produced. In addition, iPS cell lines might be similarly variable. Continue reading

Sergey Brin goes mobile in 2000 & a Russian lesson

Sergey Brin, Google co-founder is a very interesting man. His story is the number one immigrant success story in the USA today, I dare say. I have 2 Brin videos to show you today:

In the first one, Sergey demonstrates mobility in 2000 in 3 ways with his ‘faint accent that is no longer identifiably Russian’ (I really like this presentation as you can learn many things on how to give and not to give a talk):

In the second video Sergey speaks in his native language, Russian but with a “huuuge american accent” as a Russian colleague of mine wrote to me in an email. Continue reading

Biomedical informatics and the NIH, in the Googleplex

“I feel like I am talking to an empty room. Why do I feel like I am talking to an empty room?” starts Michael Marron his Google Tech Talk on NIH and the computational infrastructure for biomedical research rather unfortunately. (I remember that room.) Continue reading