BioBarCamp in the Valley before the SciFoo Camp!

It seems that my favorite ever unconference, the SciFoo Camp will be aroundunconferenced by a BioBarCamp this year. The whole idea of the BioBarCamp is based upon the SciFoo Camp, so it is by no means a competitive but a complimentary event.

From the BarCamp wiki: “The BioBarCamp is an idea (fed by the tweets of the BioTwitterer community) to organize a life sciences - biotechnology - personalized genomics & medicine - bioinformatics unconference at the Bay Area around the 3rd SciFoo Camp time, which is 8-10th August. The SciFooCamp generates a lot of enthusiasm & activity but not just for those who are invited (only 200). On the other hand, it would be nice to organize a bio-related BarCamp, just like the Cambridge BarCamb, in which the bio-related SciFoo Campers and all the other biogeeks could gather together.”

The main activity is happening right now at the public BioBarCamp Google Group. If interested please join there or just follow the discussions. We are right now in the process of finding a proper venue and sponsors and any help would be most welcome. Right now 6 or 7 August seems to be the consensus day and we have a very generous offer from The Institute for the Future via Alex Soojung-Kim Pang in Palo Alto (no response from 23andMe so far, see below).

It’s against a classic Twitter story, just like this before. You can reconstruct the whole conversation with Twitter Search Engine Tweet Scan by searching for terms SciFoo, BioBarCamp, SciBarCamp but here are my selected tweets:

Scene One, 04/10/08 How the idea was born on that day in reverse chronological order:

Scene Two 04/22/08 How the biospecificity and name was born alongside with a possible venue idea:

How to predict the future via Twitter: Google invests in Navigenics

Wow, I guess it’s time for me to move into the stock market business! Here’s the story via David Bradley’s tweet: Julie Kent, Search Engine Journal, April 21st, 2008: Google Wants to Index Genetic Information, Invests in Second DNA Start-Up

In 2007, Google made headlines when they invested $4.4 million in 23andMe, a genetic screening start-up company began by Anne Wojcicki, the wife of Google co-founder Sergey Brin, and a business partner. But if you thought that was Google’s only interest in genetics and DNA, you’re wrong. Google has also been investing in a second DNA start-up called Navigenics, which for $2,500 and a small bit of saliva will provide you with genetic test results delivered securely online containing information about the likelihood for 18 medical conditions.

What’s really funny here is that I predicted this investment last Friday, on the 18th, on Twitter. The original idea was Aaron Swartz’s Google thought experiment: Imagine you were suddenly put in charge of Google. What would you spend your time doing? I came up with this answer (picking Navigenics because of ther profile and location) on behalf of Sergey Brin:

The whole tweetstream:

Dear StartupSearch: Is 23andMe a web-based startup or not?

1. A start-up is a company with a limited operating history (Wikipedia).

2. Startup search

“tracks the web technology ecosystem commonly referenced as “Web 2.0.” We collect facts and figures about new web products, startup companies, key startup employees, and the funding dollars powering their growth.”

3. 23andMe is a pioneering web-based, personalized genomics startup (founded in April, 2006) with a high-tech service, a definitely “Web 2.0″ website & investors most Web 2.0 startups only dreaming of.

4. Why is 23andMe not tracked by StartupSearch?

What is Genentech CEO Art Levinson doing for biotech as a Google board member?

The title question is my million (not billion yet) dollar question for this year. Arthur Levinson is a board member of Google (Apple too) and in his leftover time he is the CEO of the most successful biotech company so far, that’s Genentech. I would be curious to hear about his biotech-related activity as a G board member from my readers even in the form of guesses. Maybe he is teaching biotech classes to Googlers after both Genentech’s and Google’s investment into 23andMe or just sitting around sometimes at the nice cafeterias at the Amphitheatre Parkway, Mountain View and explaining knockout technology to coders.

The second goal of 23andMe: using customer’s real health data later

Esther Dyson’s honest post on getting the genotype-health risk correlation statistics right on The Spittoon blog: What You Can Do for 23andMe (and Future Generations)

To learn more, researchers need to collect thousands of genetic profiles – and the health data connected with each of them – to find correlations between the two. That leads to a second goal of 23andMe – to collect a large database of genetic information and then come back to you over time with invitations to provide specific health data and participate in research.

We’re not asking you to do this for purely altruistic reasons - either on our part or on yours. We’re a profit-seeking company, even though our founders and employees – and directors! – all share the vision of better understanding of everyone’s genomic make-up. As for you, the research results your data help produce could translate directly into benefits for you, or at least for your children, grandchildren and friends.

Now imagine a world (2009?) in which 23andMe genotype profiles could be uploaded to your Google Health profile with one click (see picture).

Anyway, Dyson’s argument is using the “intergenerational justice” card, that is related to life extension technologies too. Dyson, an information exhibitionist also shares an interesting correspondence between her and her brother George Dyson on the growing health genomics information demand of people:

The Spittoon: the eminent corporate blog of 23andMe and Consumer Enabled Research

The personal genomics service 23andMe just launched publicly a corporate blog called The Spittoon that has been internally up for a few weeks. It is a new chapter in biotech corporate blogging. Just like the web page of 23andMe, The Spittoon’s WordPress blog platform, the concept and design is excellent: amongst others you can find scientific blog posts written by Matt Crenson science writer and posts written by founders Linda Avey and Anne Wojcicki in the name of radical transparency. As Wired fellow Clive Thompson wrote:

Radical forms of transparency are now the norm at startups - and even some Fortune 500 companies. It is a strange and abrupt reversal of corporate values. Not long ago, the only public statements a company ever made were professionally written press releases and the rare, stage-managed speech by the CEO. Now firms spill information in torrents, posting internal memos and strategy goals, letting everyone from the top dog to shop-floor workers blog publicly about what their firm is doing right - and wrong. Jonathan Schwartz, the CEO of Sun Microsystems, dishes company dirt and apologizes to startups he’s accidentally screwed. Venture capitalists now demand that CEOs be fluent in blogspeak.

Radical transparency could be standard in the case of Silicon Valley tech startups but in the Biotech Industry the standards are light years away from that. For instance the 23andMe research team communicates publicly on the biparental inheritance of mitochondrial DNA which is a sensitive issue concerning their genealogy service. The reason why Spittoon is so web-friendly and uptodate and is in fact a paradigm corporate blog for every other biotech company in the future is its web-based business model and Google-like corporate culture thanks to its networking background.

For instance, Anne Wojcicki co-founder introduces the concept of Consumer Enabled Research in her introductory blog post The Power of We:

Our goal at 23andMe is to enable individuals to form communities around shared interests and to empower those communities to be actively involved with research. We call it Consumer Enabled Research. We don’t just want communities to have a voice, we want to provide a platform for them to collectively aggregate their genetic information. One of the significant bottlenecks in research is the lack of data. Researchers and physicians rarely have enough of it to really understand a disease or how to treat it. Our goal is to change that.

After registration readers can make comments and I strongly hope that the comment system will not be shut down (just like in the past at BoingBoing), but for that commenters should be on-topic and moderate. I’ve just commented Wojcicki’s post, but I’d like to share it with you here too:

23andMe on the biparental inheritance of mitochondrial DNA and more

In my former blog post inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa? I meditated on 23andMe’s capability of detecting paternal mitochondrial DNA in their customers’ saliva with their Illumina microarray chips scanning around 2000 mitochondrial single nucleotide variants. Published here the initial answer of the 23andMe Editorial Team to this fairly technical, but nevertheless crucial question with permission granted. Besides, I am happy to report that I am working on a blogterview with one of the key member of 23andMe’s Research Team. Hopefully I’ll be able to get back to you with some first-hand information on the science and technology behind the personal genome service of 23andMe and on how 23andMe can facilitate academic research.

Dear Attila Csordas,

Thank you for your interest in 23andMe’s research mission. The question of paternal inheritance of mtDNA is a fascinating one, and the debate in the literature has continued over the past couple of decades. Currently, there is little evidence for paternal inheritance of mtDNA, outside of isolated individuals. However, the array platform lets us resolve multiple SNP states independently. 23andMe’s technology and throughput may indeed provide a novel way to address the question. We will include the question in our consideration of research projects. In the meantime, here are a couple of articles discussing the subject:

Bandelt et al., “More evidence for non-maternal inheritance of mitochondrial DNA?”
Chinnery, “The Transmission and Segregation of Mitochondrial DNA in Homo Sapiens” in Human Mitochondrial DNA and the Evolution of Homo Sapiens.

Sincerely,

The Editorial Team at 23andMe

The question is crucial for a personalized genetics company like 23andMe providing Maternal Ancestry Tree service for the customers based on the exclusively maternal inheritance of mitochondrial DNA. As one of my correspondent partner wrote:

inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa?

Have you ever asked any important but infrequently asked questions? Have you ever heard about the first personal genome service by the biotech startup 23andMe? Here is an inF.A.Q. addressed to this company:

According to the cool 23andMe genetics educator:

According to the peer review literature this is not necessarily the case and sometimes (rarely I admit) things in your cells can happen otherwise or more scientifically (mitochondrial recombination can occur):

When 23andMe’s Maternal Ancestry Tree service is tracing the genetic path of their customers, the microarray employees are identifying their haplotypes based on the differences in the mitochondrial DNA. The company is using SNPs (single nucleotide variants) unusually both from genes in the compact mitochondrial coding region (around 15.5kb) as well as within the circa 1kb large hypervariable region to give a detailed ancestry assignment. 23andMe examines few thousand places (over 2000 says Mr. Bettinger) on the mitochondrial DNA out of the total 600,000 SNPs.

But.

In the above case the 28 year old man’s blood and muscle differed at 18 positions which allowed assignment of the two sequences to separate European mtDNA haplogroups, H and U5, former being the same as the mother’s haplotype, while the haplotype of the patient’s muscle mtDNA was identical to that of his father’s and uncle’s blood. I wonder whether 23andMe’s Illumina chips can help make things clear in cases like this. (solution: let’s sequence the whole mito genome instead of a couple thousand basepairs). So as the first step in my mission to support the mission of 23andMe to support the mission of academic research I’d like to suggest putting a short tail on the possibility of paternally inherited mtDNA in the cool 23andMe genetics education material.

Pan-galactic experience: the 23andMe “official launch” webcast

Wow, what an all web experience it was: Linda Avey and Anne Wojcicki co-founders presenting their slides on the just launched personal genome service of their company 23andMe, then answering questions. The whole webcast will be available later on their website.

Here is a very short account of their webcast based on my texting and ears: Of course, they are planning to launch a blog later, they are in close contact with F.D.A. people to get things right, the genetic data on the 23andMe are belonging to customers, Google Health connection: not any right now, but open to work with anybody to empower individuals’ advance research, consumers are parts of the research process via answering surveys (so this is not really user-generated content in a Wikipedian way).

Some of my questions were connected to 23andMe’s mission to support academic research, a mission I wanted to put to the test:

- Do they plan to launch PhD programs and setting up a wholly functional research lab? Answer: a little laugh after this question and Linda Avey said something like that “oh, no, maybe later, who knows?”.

- Do they plan to organise research conferences to support research? Answer: “It’s something that we have and plan.”

My third accepted question (with a terrible English) was (the unaccepted ones were of course more intertesting.

The answer was the usual “yeah, later”.

23andMe on Pimm:

Web entrepreneurs and biotech: strangers from distant lands

23andMe: “official launch” webcast by co-founders Avey and Wojcicki

23andMe’s mission: connecting all people on the DNA level or social networking XY.0

The new faces of Silicon Valley: biotech-savvy co-founders Avey-Wojcicki

The life extension bonus effect of personal genome services: +10 years?

Spit a big in a tube, search with Genome Explorer: the 23andMe way

23andMe: the early bird of web based biotech startups

Update: Berci Meskó of Scienceroll has also been a webwitness of the Webcast.

Web entrepreneurs and biotech: strangers from distant lands

Elrond: Strangers from distant lands, friends of old you have been summoned here to answer the threat of Mordor. Middle Earth stands upon the brink of destruction, none can escape it. You will unite or you will fall. Each race is bound to this fate, this one doom. Bring forth the ring, Frodo.
[Frodo puts the ring on a stand for all to see]
Boromir: So it is true. In a dream, I saw the Eastern sky grow dark. But in the West, a pale light lingered. A voice was crying, “The doom is near at hand, Isildur’s Bane is found.”
[Reaches for the Ring]
Boromir: Isildur’s Bane…
Aragorn: Boromir!
Gandalf: speaking the words engraved on the Ring] Ash Nazg Durbatuluk, Ash Nazg Gimbatul, Ash Nazg Thrakatuluk, Agh Burzum-ishi Krimpatul.
[the light darkens and the air rumbles; Boromir backs away from the Ring]

Let us form the first real alliance of BT folks and IT people through personalized genomics (and later with regenerative medicine as I hope so), but take care, biologists and geneticists have way too powerful tools and web entrepreneurs are greedily looking for new territory with their unconceivable computational and storage capacity and perpetual hunger! Go, go, push, push! (Of course, there is no such thing as an outside threat of Mordor in this situation, the real threat (the other side of the reward coin) as in every revolutionary case is the shared ambition of tech people to make formerly impossible things possible).

The following words are from David Ewing Duncan’s Welcome to the Future:

Some analysts predict that the genetic-testing market 23andMe is entering could be worth a staggering $12.5 billion by 2009. Naturally, this has attracted the interest of Web entrepreneurs. They see an industry that is largely unregulated (so far) and costs only a few million dollars to enter—the price of a few brilliant programmers, a website, and marketing—and are betting that people will pay to test their own DNA directly.