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).
IT people are the dominant high tech tribe today and especially on the web. But biotechnology (BT) is the next infotech so no wonder that the IT crowd is growingly curious about everything biotagged on the one hand, while they are usually not too savvy in DNA-RNA-protein-organelle-cell-tissue-organ-organism related matters on the other hand. Check for instance Tim O’ Reilly at Nature: science meets bored tech-savvyness to find new things.
And what can biotech bloggers do in order to meet the growing demands: well here is a little conversation from my twitter channel in the last 20 minutes:
A partnership between the Journal of Visualized Experiments and big science publisher Wiley-Blackwell: the JoVE guys will give the technology, the art of making video experiments and Wiley provides the established network, audience on its Current Protocols site.
I wonder what will be the access status of those videos: current JoVE videos are freely available, while Current Protocols has pricey subscription rates (see screenshot).
“Rumors of JoVE’s deal with Wiley-Blackwell and other mainstream science publishers have been circulating in the blogosphere since late January. Moshe Pritsker, CEO of JoVE, told The Scientist this week that he had also signed similar deals with Annual Reviews and Springer Protocols.“
So I accepted the invitation and became an Academic Editor. But I confess that I was not yet a true convert to OA or to PLoS Biology. So I decided to do what any good scientist should do in such a situation—I planned a publishing experiment. I’d had many papers in Science and Nature before. And so I convinced my collaborators on a high-profile paper to submit it to PLoS Biology, to see how this new high-profile OA journal would compare.
But then, while finalizing the paper, a two-month-long medical nightmare ensued that eventually ended in the stillbirth of my first child. While my wife and I struggled with medical mistakes and negligence, we felt the need to take charge and figure out for ourselves what the right medical care should be. And this is when I experienced the horror of closed-access publishing. For unlike my colleagues at major research universities that have subscriptions to all journals, I worked at a 300-person nonprofit research institute with a small library. So there I was—a scientist and a taxpayer—desperate to read the results of work that I helped pay for and work that might give me more knowledge than possessed by our doctors. Read the rest of this entry »
The preliminary program already has over two dozen confirmed
speakers, all of them world leaders in their field. As for previous
conferences I have [co-]organised, the emphasis of this meeting is on
“applied biogerontology” — the design and implementation of
biomedical interventions that may, jointly, constitute a
comprehensive panel of rejuvenation therapies, sufficient to restore
middle-aged or older laboratory animals (and, in due course, humans)
to a youthful degree of physiological robustness. The list of
scientific sessions and confirmed speakers is as follows:
DNA damage, telomeres, cancer
Adam Arkin, Lawrence Berkeley National Laboratory; Jan Vijg, Buck
Institute for Age Research; Jerry Shay, U. Texas Southwestern;
Claudia Gravekamp, Pacific Medical Center Research Institute; Zheng
Cui, Wake Forest University School of Medicine; Rita Effros, UCLA
The cell niche
Irina Conboy, U. California Berkeley; Judith Campisi, Lawrence
Berkeley National Laboratory and Buck Institute; Leanne Jones, Salk
Institute; Ken Muneoka, Tulane University; Kevin Healy, Stanford
University Read the rest of this entry »
Finally back from my Bay Area trip, the workshop I participated turned out to be very stimulating in terms of people and ideas. Also visiting The Blood Knot performance at the American Conservatory Theater and having a drink with Monya&Dan were absolutely delightful. I missed my flight on Saturday, so I slept in LA (and missed my wife) and discovered the city to the amount of a Taco Bell dinner near to the La Quinta Hotel. Also I did a little geek tourism and visited the South Park area in San Francisco (but forgot to check the Wired headquarters) which was so nicely described in Aaron Swartz’s unfortunately unfinished (but not unfinishable) Bubble city:
Downtown San Francisco is a world of carefully-gridded streets and looming skyscrapers, but hidden behind a gas station on Third is a place that almost looks like another world. The sun shines brightly upon a park with green grass and tall shady trees and vibrant swings with children. The park is an oval and the perimeter is lined with small, pastel-colored buildings. Here and there are a smattering of small cafes and restaurants. And the other buildings are filled with startups. Twitter here. Adaptive Path there. Even Yahoo, when it wanted to encourage its employees to be more startup-y, opened up an office in the neighborhood. Sit on the grass and chances are you’ll sit near a friend from another company or bump into them in line at a cafe. The place crawls with companies and back on the street, surveying the scene with a distant but watchful eye, lie the journalists, whose publications cover with awe the rumblings of those below. It was here that Newsflip made its home.
Leaving New Orleans for the Bay Area for the next 3 days. I am visiting a quite enigmatic workshop in Palo Alto on Feb 22, then I am in San Francisco downtown on Friday evening and Saturday AM. If anybody would like to meet me, I am available there on Saturday near Union Square, just drop a mail.
Travel readings: Wired, March (not online yet, The Ruby on Rails coverage was interesting, but still hesitating whether to read Chris Anderson next airport book ad essay: Free or not, but definitely will read Joshua Davis story on Cougar Ace), Woody Guthrie: Bound for glory
Also a Wired recommendation: How to fly through the airport security in a dignity safe way: laceless shoes and holeless socks.
I emailed some of my life extension supporter friends because I think we have a ‘future’ situation:
Healthy life extension is not 1 out of the 14 Grand Engineering Challenges…that can be realistically met, most of them early in this century according to the Committee on Grand Challenges for Engineering with members such as Larry Page, Dean Kamen, Craig Venter, Robert Langer and …lifestyle life extensionist, nanovisionary Ray Kurzweil. There is a challenge though called Engineer better medicines and the essay behind looks as if it had been hacked together by Kurzweil and Venter themselves during a sunny Californian Soy Beer Baby Boomer Beach Party. It is about personalized medicine in large and the only hint – I was able to find – to a recent discipline named regenerative medicine is a paragraph, not on, say the challenge of systemic regmed, but on synthetic biology.
It is a big challenge to learn how could healthy lifespan extension as a big and realistic challenge have been left out? Why did Kurzweil (author of the book Fantastic Voyage: Live Long Enough to Live Forever) not stand up for it? Why nobody out of the luminaries thought that regenerative medicine and stem cells worth discussing more than a tiny side note? And what about Venter, whom I still like to be interview as there are many points in his activity suggesting a life extension connection. Somebody in the committee was clearly against it?
One friend told me that he is not surprised by this, because it was announced at the AAAS meeting, which is very conservative. Out of the committee members Ray Kurzweil, Daniel Hillis, and maybe Dean Kamen would have been supporters of including LE as a challenge.
For historical reasons the standard human mitochondrial sequence, the Revised Cambridge Reference Sequence (rCRS) is a reconstruction of a single European individual’s mtDNA and contains several rare alleles. That’s why many times a usual mtDNA sequence alignment must appeal to phylogenetic historical reconstructions. The rCRS nevertheless provides a uniform nucleotide numbering scheme (0-16569). On the other hand, as there are thousands of high-quality, full-length mitochondrial sequences are now available, Robert Carter thought that it is time to construct and analyze a comprehensive human mitochondrial consensus sequence and published his efforts in Nucleic Acid Research, March, 2007: Mitochondrial diversity within modern human populations The sequence itself available as a supplementary material but with the permission of the author I copy it into this post below.
According to Robert Carter:
So far, all feedback has been good. By introducing the idea of “poly-x” sites (see later), I successfully created a technique that avoids all pre-conceived ideas about genetic history. This also allows one to effectively deal with indels, something that many authors have avoided in the mtDNA literature.
Briefly, 827 sequences were used, a master sequence alignment was created in BioEdit and BioPerl was used for all calculations using the rCRS asa template for nucleotide numbering. Read the rest of this entry »
One friend of mind is looking for a proper double staining protocol for laminin and BrdU on fixed rat striatal muscle slices. Can anybody help, please?
I’ve just noticed a New York Times paid “stem cell research” Google Adwords ad in my gmail inbox besides the automated “Rejuvenation Research Vol. 11, No. 1, Feb 2008 is now available online” mail. That said, The New York Times is ranking the “stem cell” buzzword high and fishes for layman readers interested in the whole regmed topic for its own stem cell site both in the search results and next to articles (in the content network – explains Anna, my online marketer wife, next to me). I wonder for how long they have been paying for these ads? Other mainstream journals have similar ads, like The Washington Post. C’mon folks, let’s spend a part of those ad dollars to real stem cell research too!!!
…that can be realistically met, most of them early in this century according to the Committee on Grand Challenges for Engineering with members such as Larry Page, Dean Kamen, Craig Venter, Robert Langer and …lifestyle life extensionist, nanovisionary Ray Kurzweil. There is a challenge though called Engineer better medicines and the essay behind looks as if it had been hacked together by Kurzweil and Venter themselves during a sunny Californian Soy Beer Baby Boomer Beach Party. It is about personalized medicine in large and the only hint – I was able to find – to a recent discipline named regenerative medicine is: Read the rest of this entry »
Last time I said: Although the paper was retracted from the online version of Proteomics, you can still make historical screenshots on the PubMed version.
Now the chance is over. But what is really funny: finally, PubMed ‘Related Links’ algorithm gives us the proper context of the Warda-Han-Mighty paper, just take a look at the first 2 related articles on the right:
However the paper was only retracted for “a substantial overlap of the content of this article with previously published articles in other journals.”, not for the strange “mighty creator” line. Peer review isn’t perfect but you’d hope it would catch something like this.
The Warda-Han-Proteomics saga continues and finds its way to the show/entertainment business. We’ve already listened to Han, now it’s time for Warda to speak, which he did in an email to James Randerson over at the Guardian Science blog, which makes think (indeed ‘rethink’ as W suggests) that the Warda-Han pair is probably the Laurel and Hardy of the science showbiz.
Have you ever wanted to isolate subcellular components from molecules to organelles with the old but ever improving ultracentrifuge method but were unable to figure out a correct protocol as the basics were not that clear?
To get an optimal protocol you have to take account the biological entity and pellet you want, the maximum volume input you need, the rotor and pathlength available in the lab and the time you have for all this.
Lately I’ve learnt the basics of ultracentrifugation from Richard Sicard (Thermo Scientific) who was nice enough to send me an excellent educational material called Ultracentrifugation: Basic Training from Thermo Fisher Scientific also giving me the permission to share it. I’ve chosen 14 slides. If you need a bigger resolution (especially on slide 2, 4), go to the Slideshare version and click full.
First of all: thanks to the commenters/scientists (the online flash mobbers) for being the most efficient part of the science blogosphere! Although the paper was retracted from the online version of Proteomics, you can still make historical screenshots on the PubMed version.
Colbert: “But if people lived to be a 1000 years old won’t that kill any ability for humans to take risks cause if I’ve known I lived to be a 1000 I am not going to cross the street because you can’t cure being hit by a bus.”
Aubrey: “Well, you’ll be able to get your grandmother to help you to cross the street.”
That is a witty (and the same time, deep) answer indeed: People usually help their grandmother to cross the street but in a many generational “rejuvenated” world people will be able to take care of their descendants to the same extent as they are able to take care of their ascendants today. Moreover, it has something to do with the philosophical question of intergenerational justice: Read the rest of this entry »
Genome Technology, the heavy trafficked New York based biotech website (also a printed monthly magazine) just launched the beta version of MethodShare as “a place for people to discuss methods and tools, recommend methods papers to one another” according to Ciara Curtin, senior editor. The site will be coming out of beta soon.
How the site can position and maintain itself in the narrow space between the professional Connotea reference manager on the one hand and the versatile high end methods site ranging from Nature Protocols to JoVE on the other hand is a really open question at this point. This won’t be a simple game and good luck to them.
We have now a well-developed and sad case example of irresponsible scientific editing and publishing: the Warda-Han advanced online paper by the academic journal Proteomics: Mitochondria, the missing link between body and soul: Proteomic prospective evidence. What started as an abstract-based hunch and question about the quality of a recent review, addressed to and amplified by the the scientific blogosphere may probably end as a piece of investigative journalism in the mainstream media with serious consequences and conclusions on scientific publishing. Right now, the real investigation takes place at the comment section of the PZ Myers post A baffling failure of peer review over at Pharyngula. The story there is quickly unfolding thanks to the smart and open-eyed (Google-savvy) contributors who figured out amongst others that Warda and Han significantly reduced their review writing efforts by borrowing many sentences from other colleagues’ papers. Here I’d like to mention and cite only 3 comments: Read the rest of this entry »
Creationism/intelligent design is not really an issue for me as I am a biologist working with mitochondria and stem cells, also a life extension supporter, whose angle on things and projections are based on the recent advancements in science and technology. As far as I know, creationism/ID neither suggests any new experiments or heuristic solutions in my research field, nor does it help to plan&build new technologies to extend healthy lifespan. From my point of view, thinking about creationism is a waste of valuable scientific/technological processor time.
Last week when I wrote the post Can you tell a good article from a bad based on the abstract and the title alone? on the review I had only 10 minutes for figuring out the post between 2 experiments in the lab during lunchtime. The only thing that came into my mind reading the abstract – popped out of PubMed feeds – was that something stinks here. Now it’s Mardi Gras day and I have a couple of minutes more to address this issue and hopefully no more.
Myrmecologist and blogger Alex Wild picked one sentence from the paper in a comment, and here is the complete paragraph:
Alternatively, instead of sinking in a swamp of endless debates about the evolution of mitochondria, it is better to come up with a unified assumption that all living cells undergo a certain degree of convergence or divergence to or from each other to meet their survival in specific habitats. Proteomics data greatly assist this realistic assumption that connects all kinds of life. More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life.
This is the closing paragraph of the section Mitochondrial integrated function disproves endosymbiotic hypothesis of mitochondrial evolution. The mitochondrial part of the well established evolutionary endosymbiotic theory claims that ATP-producing mitochondria were ancient prokariotic invaders of host prokariotic cells eventually turned out to be the common ancestors of eukaryotic cells. I always found this hypothesis one of the most fruitful scientific concepts as it constantly suggest new ideas and warns that current eukaryotic cells are the products of an evolutionary, accidental and instable alliance between the mitos and their hosts. As the endosymbiotic theory is the mainstream academic theory of mitochondrial evolution it is a challenge for scientists to attack it with counterarguments and that’s what Warda and Han are aiming for in that section. What they are doing seems like a legitimate discussion of a scientific theory but ends with the logically unacceptable jump to the fingerprints of a mighty creator as an alternative explanation.
Before I cite the section in question in full length and recommend to my readers to analyze it, I also like to suggest the detailed comment of D. Spencer saying amongst others:
If Wiley and the journal Proteomics allow this into print (it is currently only “published” online) they can kiss goodbye to any hope that Proteomics will ever again be regarded as a serious scientific publication.
Here is the complete section by Warda and Han without references that could be found in the full text: Read the rest of this entry »
Yesterday we watched the movie Enigma, and it is first-class as entertainment although not well-known. I became interested in it as Tom Stoppard wrote the script and my favorite movie ever is Rosencrantz and Guildenstern dead. Mick Jagger was the producer of the movie and he also appears for a sec as a background English soldier (captain?) with 2 ladies and a cigarette.
MitoWheel is a cool graphical interface of the circular human mitochondrial genome, which helps the user to get familiar with the mito DNA by searching, clicking and tailoring it. I introduced you MitoWheel a week or so ago, but now you can follow the updates on the MitoWheel Blog.
On the blog you get first-hand information as the posts are written by Gábor Zsurka, main developer himself and occasionally, by me. In his post Cut and Paste the Human Mitochondrial DNA Gábor introduces 2 essential techniques you can easily accomplish with MW:
a., how to search for different mutations and find their functional results on a pop-up window
The pioneer biological video publishing site JoVE (covered here many times) will soon launch a blogging platform and a community site. Nikita Bernstein, the main nerd behind JoVE is building the code and the platform – as Anne Kushnir informed me – should hopefully go live in the next couple of weeks. At least that is what can be known publicly.
The expectations are high and the JoVE guys (co-founders Moshe Pritsker and Nikita) themselves raised the bar with the quality and concept of video-protocols. As JoVE is a startup, not an established company with big inertia, they could be experimental but within the limits of their investors’ patience and money.
The real question for me whether JoVE’s blogging service can renew the genre of science blogging or at least bring a previously non-existing color into it? Points:
- Who will become JoVE’s first generation bloggers? Fresh blood? If yes what will be the source? Senior scientists, high school students, postdocs in the U.S.A., discovering the web?
- Existing bloggers who’d like to syndicate their content? Bloggers from Scienceblogs, Nature Network or from the DNA Network? Independent bloggers from outside theses established circles? Journalists? What will be the bait? For existing bloggers, who are tempted to commercialize their activity somehow the crucial question is whether they can generate any revenue out of this new platform? Will they be paid by traffic, and if yes how competitive are the tariffs? Is it possible to install paid ads, banners on the blogs and the bloggers could be paid based on pay per click methods just like Google AdSense?
– What about content rights? Exclusive, non-exclusive, et cetera? Would there be any topic restrictions? How can quality science blogging and credit is maintained in the long term? Read the rest of this entry »
Have you ever wanted to isolate subcellular components from molecules to organelles with
the 
