Posted by attilacsordas on October 31, 2009
The LavaAmp is a portable PCR thermocycler that has the potential to become the default garage biology (home biology, bioDIY, DIYbio) tool once it hits the market. Think of Apple II for personal computing or MakerBot for 3D printing.
The 1st LavaAmp prototype was shipped this week from Biodesic to Gahaga Biosciences and the process is documented and engineering details uncovered in Rob Carlson’s post.
The people behind are mainly ex SciFoo Campers and open science advocates: Guido Nunez-Mujica, Joseph Jackson, Rob Carlson, Jim Hardy and a cool engineer Rik Wehbring.
Here’s the pic of the prototype:
In the 2007 proof-of-concept paper, entitled A Pocket-Sized Convective PCR Thermocycler, authors Nitin Agrawal, Yassin A. Hassan, and Victor M. Ugaz wrote:
Herein, we introduce an innovative thermocycling system that
harnesses natural convection phenomena to amplify DNA rapidly by the PCR in a greatly simplified format. A key element of this design is an architecture that allows the entire thermocycling process to be actuated pseudo-isothermally by simply maintaining a single heater at a constant temperature, thereby enabling a pocket-sized battery-powered device to be constructed at a cost of about US$10.
Realizing the potential of the device and thinking about how to build a digital thermocontroller for it with the Arduino I contacted Victor Ugaz this January and was informed that they only built the proof-of-the-concept devices testing them in the lab interested mainly in ‘understanding the physics of the thermally driven flow and its effect on the reaction’. But it was obvious to me that somebody will produce those devices for the market and make them affordable to people as it seemed to me as the familiar case of the low(est)-hanging-fruit.
So when Joseph Jackson mentioned to me his grandiose open science plans and the groups’ ‘super affordable pcr’ project I became instantly interested. As Rob Carlson writes:
The intended initial customers are hobbyists and schools. The price point for new LavaAmps should be well underneath the several thousand dollars charged for educational thermocyclers that use heater blocks powered by peltier chips.
Posted in biodiy, biohacking, biology, biotechnology, diy, DNA, geek, open science, Sci Foo, science, science hacks, SciFoo | 110 Comments »
Posted by attilacsordas on October 21, 2009
Kaiser Permanente alongside with UCSF plans for genetic analyses of an unprecedented 100,000 older Californians, the Technology Review writes in Massive Gene Database Planned in California
The effort will make use of existing saliva samples taken from California patients, whose average age is 65. Their DNA will be analyzed for 700,000 genetic variations called single-nucleotide polymorphisms, or SNPs, using array analysis technology from Affymetrix. Through the National Institutes of Health (NIH), the resulting information will be available to other researchers, along with a trove of patient data including patients’ Kaiser Permanente electronic health records, information about the air and water quality in their neighborhoods, and surveys about their lifestyles.
The target age group shows that the focus is on “secondary aging”:
Given the high average age of the group, the platform will also be a boon to studying diseases of aging. “One might want to ask,” Schaefer says, “what are the genetic influences on changes in blood pressure as people age, and how are those changes in blood pressure related to diseases of aging, like stroke and Alzheimer’s and other cardiovascular diseases?”
UCSF will perform separate procedures on the samples to determine the length of telomeres–sections of DNA at the ends of chromosomes that protect against damage. The length of telomeres is associated with cell division and aging. One of the coinvestigators on the project is Elizabeth Blackburn, a biologist at UCSF who shared the 2009 Nobel Prize in Medicine for her work on telomeres.
Posted in aging, california, genetics, genomics, science, USA | 15 Comments »
Posted by attilacsordas on October 8, 2009
Sage Bionetworks is a not-for-profit organization developing an open-access “pre-competitive” platform for networked and annotated models of human disease. It’s a huge and unparalleled bioinformatics enterprise: starting with an anonymous $5 million donation and soon making high throughput, large-scale human and mouse biological data (largely from Merck) available in the range that’s already in the public domain today. The co-founders are real big shots, Stephen Friend, a former successful Merck Executive and Eric Schadt, now a Chief Scientific Officer of Pacific Biosciences, who is “an industry leader in network biology with a number of high-profile publications over the past 5 years that have energized the systems biology community.”
For the last couple of months there was only minimal information available on the Sage website but now scientists interested can get the big picture in more details via a significant update.
The strong motivation behind is to build an open-access standard platform for human disease biology because
human disease biology has no common languages, no accessible communal repositories and no government, corporate or foundation investment in generating an inclusive resource….The experimental data underlying disease biology, like the genome itself, needs to be open access because the data is simply the beginning of the process….
Human disease biology is so complex, interconnected and expensive to research that the existing dominant business strategies of building and patenting unique models need to be replaced by a common standard. Like the internet, disease biology models will gain strength by their very nature as public platforms for interoperability and communication – this approach is at the very heart of that strength.
At the heart of the Sage model are the so called Global Coherent Datasets that will be for the first time available for scientists working all around the world. We’re talking about a real goldmine here for researchers:And if that doesn’t sound good enough for a start then the following Sage Datasets will be available in 1 to 2 years: Read the rest of this entry »
Posted in bioinformatics, biology, science, USA | Tagged: sage | 18 Comments »
Posted by attilacsordas on October 5, 2009
“for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase” press release
The award goes to Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak.
The problem of telomere/telomerases is highlighting the double but strictly related aging/cancer problem space:
Posted in aging, cancer, cell biology, science marketing | 16 Comments »
Posted by attilacsordas on September 16, 2009
Big news at PLoS: today Mark Patterson announced on the PLoS blog that
“As part of our ongoing article-level metrics program, we’re delighted to announce that all seven PLoS journals will now provide online usage data for published articles”.
I downloaded the entire dataset and as a starter sorted it according to Combined Usage = numbers of HTML page views (the full text version of our articles) + PDF downloads + XML downloads
Here is the Top Ten most viewed PLoS articles according to the newly released article-metrics (read the FAQ too).
Posted in open-access, science | Tagged: Plos | 17 Comments »
Posted by attilacsordas on May 3, 2009
Nature’s Journal Club column is usually a good & always a short read providing exciting angles on scientific topics/papers from good researchers. Recently ‘neuroscientist’ Dave Featherstone argued for a broader approach to brain mapping by not restricting it only to the connectome between neurons. Neurons are making up less than 10% of the human brain while most brains cells are glia neglected by scientists making the wiring diagram of a ‘complete’ human brain.
For example, consider the recent study of adenosine and sleep led by Philip Haydon and Marcos Frank at the University of Pennsylvania in Philadelphia (M. M. Halassa et al. Neuron 61, 213–219; 2009). Adenosine binds to receptors on neurons, thereby regulating neuronal signalling. Interestingly, adenosine seems to represent ‘sleepiness’: it accumulates during wakefulness and dissipates during sleep. Where does it come from? It is generated from adenosine triphosphate (ATP), which is secreted by astrocytes — a major type of glia.
Therefore, if we want to map the functional brain connections controlling sleep, we need to include glia and the extracellular space between glia and neurons. If we’re going to understand brain function by mapping the brain, we need to include most of the brain in our map.
I tried to draw an analogy between the situation in brain mapping and personal genomics on FriendFeed:
Update: it seems Dave Featherstone had something similar in mind as an analogy, he answered my email the following way:
Yeah, that’s a good analogy. The original version of my column said the connectome would be like if the human genome had only sequenced exons. But that sentence was cut for space considerations.
Posted in biology, genomics, Nature, neural, personalized genomics, science | 10 Comments »
Posted by attilacsordas on April 7, 2009
Last Friday 23andMe came up with Haplogroup Tree Mutation Mapper which is the first experimental feature that can be instantly tested by biogeek customers (a large portion of the company’s customer base) in its freshly launched technology sandbox 23andMe Labs that is much like Google Labs.
Haplogroup Tree Mutation Mapper “shows you which particular mutations in a person’s mitochondrial DNA (maternal ancestry) or Y chromosome (paternal ancestry) were used to determine their haplogroup assignment.”
Basically you are picking the Y chromosome or type the name of a maternal mitochondrial haplogroup (like T) into the search box and as a result you get a list back with the position and id-s of the defining mutations. With that information you can play different genetic genealogy games if you like.
But playing with a pure textual list of SNPs doesn’t sound too fascinating and the tool is not really a “Mapper” as there’s no visualization included. Wouldn’t it be nice if you can visualize all those haplogroup defining SNP positions at once and get extra biological information on them right away? Well, you cannot do that within the 23andMe website but you can do that with Mitowheel which is a graphical representation of the circular human mitochondrial genome (Disclaimer: I am part of developer team, see post and the Mitowheel blog).
For instance the SNPs on the left are parts of the T haplogroup defining mutations used by 23andMe. The rCRS is the revised Cambridge Reference Sequence, the rs<numbers> are the reference cluster IDs of SNPs. rCRS is a reconstruction of a single European individual’s mtDNA, the source was an unnamed placenta without further identity and it contains several rare alleles. I’ve also heard rumors that some blurry nucleotides were replaced by cow DNA. The rCRS nevertheless provides a uniform nucleotide numbering scheme (0-16569) even if the 3106 position is a phantom position (like chief evangelist) as there was an incorrect duplication of 3107C in the original sequence. So if you check the rCRS positions on the list, the one you should use in Mitowheel is +1 position away that you can see in parentheses if you click on the individual SNP rsids within the 23andMe site.
So here are all the positions 23andMe is using for T haplotyping and you can type them into the Mitowheel search box: 10463, 13368, 14905, 15607, 15928, 188, 4917, 709, 8697 and step through all of them by clicking the arrow in the search box and get a lot of extra information by checking the info popup box.
As a 23andMe customer you can instantly look for functional information on your particular SNPs with Mitowheel by adding the nucleotide letters of your specific mutation to the positions like in 8697A, so the following is the result of the search for all of my T defining SNPs: 10463C, 13368A, 14905A, 15607G, 15928A, 1888A, 4917G, 709A, 8697A
As Mitowheel incorporates data on fully sequenced human mitochondrial genomes that have been deposited in the GenBank database the allele frequencies of 23andMe customers can be checked at those positions and groups can be created based on Gábor Zsurka’s, Mitowheel founder, post. Read the rest of this entry »
Posted in 23andMe, genetics, genomics, mitochondria, mitoWheel, personalized genetics, personalized genomics | 33 Comments »
Posted by attilacsordas on March 10, 2009
Surprise email from Conor McKechnie, GE Healthcare proving the aesthetics of science and the value of blogging:
A while (!) back you posted an inspiring piece linking to Harvard’s BioVisions inner life of the cell – it was 2006…It got me thinking that we could do something similarly inspiring with actual cellular images entered into our annual cellular analysis image competition. It took 2 years to make it happen, but finally:
We have just posted a social media release highlighting the winners’ images being shown on the jumbotron in Times Square, with a short narrated film about the images and what they could mean for medical research, posted on YouTube:
Video interviews with the winners in Times Square on YouTube:
Short listed entries on a public site to inspire and encourage people to share in the beauty of science.
I hope you enjoy the links – and thanks for being the initial spark of inspiration.
Posted in biology, image, innovation, New York, photo, science animation, science marketing, USA | 6 Comments »
Posted by attilacsordas on March 3, 2009
Let us assume that you are a technological early adopter, a maker, a hacker, a geek. Your software/hardware skills and experiences are much better than the bulk of licensed physicians. You also have a G1.
Now imagine a mobile application/gadget-in-a-belt-pouch that is the most advanced telemedicine solution in the market. With this application/gadget you were able to non-invasively monitor vital signs of the people that matter you the most at anytime from anywhere around the world. You were able to quickly recognize life threatening heart and respiratory problems of the people you care about and maybe save their lives.
The problem is that such a product exists according to this press release (via androidguys) but you are not allowed to legally use it (no information on the details of purchase yet) unless you are a registered and licensed physician. The press release does not offer any reasonable (legal?) explanation on why this is the case.
The Dyna‐Vision© G1 Android Telemedicine Application by RS TechMedic B.V (“specialized in creating very easy-to-use user interfaces”) will be officially launched during the CeBIT starting today:
Dyna‐Vision© is a small light weight and portable device, with the dimensions of a PDA. The patient wears this device in a belt pouch. This reliable and sophisticated medical device monitors up‐to 10 clinical parameters through non‐invasive sensors attached to the skin. The measurements include 12‐lead ECG, Heart Rate, Heart Rate Variability, RR‐times, Respiration, Plethysmogram and Oxygen
Dyna‐Vision© automatically transmits cardiac events and even continuous real‐time ECG recordings to a secured server. Besides using a computer or laptop, physicians can now also monitor a patient’s real‐time vital signs on a G1 Android mobile phone. Physicians can use the application at anytime from anywhere around the world.
The Dyna-Vision G1 Telemedicine Application can only be used by licensed physicians after registration with RS TechMedic B.V.
Posted in biodiy, diy, future, gadget, geek, medicine, regulation, technology | Tagged: Android | 14 Comments »
Posted by attilacsordas on February 28, 2009
Take a look at the FDA Application Approvals 2000-2008 visualization (created by user mktlgcs) over at IBM’s Many Eyes to get an aerial view on the US. pharmaceutical industry.
Posted in biotechnology, FDA, industry, US, USA | 16 Comments »
Posted by attilacsordas on February 5, 2009
Forbes article: Letting Google Take Your Pulse via @mattcutts:
On Thursday, Google and IBM will unveil a new initiative that will allow Google Health, a site where users can store and track information about their medical history, to connect to and stream data from medical devices. In demonstrations, IBM and Google fitted Wi-Fi radios to gadgets like heart rate monitors, blood pressure cuffs, scales and blood-sugar measurement meters, allowing the devices to communicate with a PC and feed real-time medical information directly into Google’s online records.
Hooking up those devices to the Web, IBM argues, will offer a new immediacy and granularity of health monitoring. A user can remotely track the blood pressure readings or glucose levels of a diabetic parent living alone, or stream his or her medical information like weight or heart rate directly to a doctor or physical trainer.
“If there’s something abnormal, you can catch it before you have an episodic intervention, like going to the emergency room,” says Dan Pelino, manager of IBM’s health care division. “This is like OnStar for a patient, keeping constant information about you and sending alerts even before you have a problem.”
More on Google Health on Pimm:
Meet Dr. Google Health: Roni Zeiger, right from Stanford!
Google Factory Tour of Health: watch the pivotal moment!
FriendFeed comments: The hidden backyard
Late Google Health: catching up with the past, first!
A bit of history: The official launch of Google Health, 19/05/08
Posted in partial immortalization | 12 Comments »
Posted by attilacsordas on February 1, 2009
The folks at The Institute for the Future have been busy lately and as a result Signtific has been launched replacing ScienceX2! Check this, the about and FAQ pages if it’s new to you or just simply explore.
Posted in science, Silicon Valley, technology, The Institue For the Future, USA, X2 | 4 Comments »
Posted by attilacsordas on January 29, 2009
After the Nature cover article Hugh Rienhoff and the story of My Daughter’s DNA is now covered by Wired magazine. I wrote about Hugh (a fellow SciFoo Camper) as an example of any future bioDIY effort in The conditions of a mass biotech DIY movement and now the Wired piece gives us more context and details concerning how things were actually done. This is really a story that cannot be overemphasized by simply telling it again and again.
By making inquiries with local surplus brokers, Rienhoff discovered he could buy a secondhand PCR machine for less than a MacBook. He ended up purchasing a full working model for just $750.
Obtaining additional supplies, like the PCR reagents, for his experiment was tougher. Some chemical companies didn’t want to ship to a private address, so Rienhoff pretended his house was the headquarters of the fictional Institute for Future Study.
While Rienhoff could spring for his own PCR machine, a used gene sequencer (assuming he could find one) would cost around $100,000. So he found a university lab (which he declines to identify) that would sequence the genes he had amplified, for $3.50 per 50-microliter sample. In spring 2007, Rienhoff mailed in more than 200 samples.
Rienhoff compared Beatrice’s DNA with the information on Ensembl, looking for any base-pair variants that hadn’t been previously recorded on Ensembl. Read the rest of this entry »
Posted in biodiy, biohacking, biology, diy, genetics, genomics, medicine, science hacks | 8 Comments »
Posted by attilacsordas on January 15, 2009
Friend Dan Erlanson (Co-Editor in Chief of the niche and smart Fragment-based Drug Design blog Practical Fragments) sent me this story on the recession proof business model of a biotech company called BioBlocks and his founder medical chemist Peter Pallai:
Approximately one out of 5,000 compounds pass an initial screen, hit the designated biological target, and end up making it to clinical trials. So Pallai’s pitch is simple. He and his team are good at one thing-chemical synthesis of new drug candidates to hit those targets. By outsourcing this piece of the puzzle to his team of chemists, about 25 of whom work in Budapest, Hungary, biotech companies can get the work done fast and well, he says. It makes sense professionally for his chemists as well, because they can get steady work, rather than hitch their wagons to one of hundreds of biotechs that dream of becoming the next Genentech, but are more likely to end up flaming out in a few years.
Posted in biotechnology, industry, innovation | 15 Comments »
Posted by attilacsordas on December 16, 2008
The first Euro Maker Faire in Brussels was an evening event but now with the first UK Maker Faire makers have a chance to hang around for 2 days and develop or deepen their DIY skills similar to the original US events (we enjoyed Austin Maker Faire in 2007). Let me know if you’re interested.
from my mailbox:
We are shortly to publicly announce the first UK Maker Faire but thought you would appreciate advanced notification.
The Make team forwarded me your names and email addresses as they believe you might be interested in the Newcastle upon Tyne Maker Fair on March 14th-15th 2009.
The first UK Maker Fair will take place in Newcastle 14-15 March as part
of Newcastle ScienceFest – a 10 day festival celebrating creativity and
This two-day, family-friendly event celebrates the Do-It-Yourself (DIY) mindset and features interactive exhibits organized by individual enthusiasts, hobbyist groups and clubs as well as student groups. It’s for creative, resourceful folks who like to tinker and love to make things. Maker Faire is an opportunity to share what you do with others. Read the rest of this entry »
Posted in biodiy, diy, geek, MAKE, open science, open source, science, science hacks, technology, UK | 7 Comments »
Posted by attilacsordas on December 15, 2008
In the past months Thomas Goetz begun writing a book on the radical changes already ongoing but mostly upcoming in healthcare due to affordable new technologies and quantitative approaches in personalized genomics and medicine.
The book is to be called The Decision Tree (explanation below) accompanied by a new website. Thomas is the perfect man for this job, he is the deputy editor of Wired magazine (=he is well informed and connected), a good journalist who took his job (writing on science, health and medicine) so seriously that he went back to school to get a degree in Public Health. Back in the days his very early coverage on 23andMe (actually published before the official launch of the service) was actually the only serious insight on 23andMe.
With this book Thomas will have a chance to become the Chris Anderson or Malcolm Gladwell of personalized medicine and public health.
“The premise is that we are at a new phase of health and medical care, where more decisions are being made by individuals on their own behalf, rather than by physicians, and that, furthermore, these decisions are being informed by new tools based on statistics, data, and predictions. This is a good thing – it will let us, the general public, live better, happier, and even longer lives. But it will require us to be stewards of our health in ways we may not be prepared for. We will act on the basis of risk factors and predictive scores, rather than on conventional wisdom and doctors recommendations. We will act in collaboration with others, drawing on collective experience with health and disease, rather than in the isolation and ignorance that can come with “privacy” concerns. And we will act early, well before symptoms appear, opting to tap the science of genomics and proteomics in order to mitigate our risks down the road.
Together, these tools will create a new opportunity and a new responsibility for people to act – to make health decisions well before they become patients. This can be characterized as a decision tree, a series of informed choices we will make to minimize uncertainty and optimize our outcomes. Indeed, we will use decision trees to navigate most of our health decisions, sometimes in overt ways – new decision support tools will both inform us and guide us, and they’ll be steeped in statistics, prediction, and the power of collective experience.”
Posted in 23andMe, biotechnology, blog, journalism, personalized genetics, personalized genomics, personalized medicine, Wired | 19 Comments »
Posted by attilacsordas on December 11, 2008
Nature’s newest issue has a Quantitative genetics supplement with 3 free access pieces included out which I find this review the most interesting: Reverse engineering the genotype–phenotype map with natural genetic variation by Matthew V. Rockman. There’s a lot information to digest and many patterns to understand in this background field in order to approach the future of (personal) genetics/genomics.
Posted in biology, genetics, Nature, open-access, science, UK | 7 Comments »
Posted by attilacsordas on December 8, 2008
After the first Twitter prediction here is my second one back from September, realized today:
and here we go….Happy Holidays Grandma you’got a 2fold risk for psoriasis but don’t worry too much about the Alcohol Flush Reaction and your caffeine consumption!
Actually I tried to convince Read the rest of this entry »
Posted in 23andMe, marketing, personalized genetics, personalized genomics, Twitter | Tagged: 23andMe, Christmas gifts, personal genomics, Twitter | 7 Comments »
Posted by attilacsordas on November 18, 2008
How do you interpret the following situation: we have a life extension technologist whose all endeavors is about pushing this issue to its very limits and making things possible but on the other hand this very life extensionist himself is not driven by actually living as long as he can.
It seems that SENS theorist Aubrey de Grey, who is chronologically 45, (BioBarCamp photo by Ricardo) is taking roughly the above position in a recent interview. Aubrey is a good and witty interviewee and of course the interpretation of what he is saying is strongly context dependent so here is the full question and answer:
Question: One hundred years of life can wear you down physically, but it can also wear you down emotionally… perhaps even existentially. For you, is a desire to live long accompanied by a desire to live long in a much-improved human civilization, or is this one satisfactory?
Aubrey de Grey: I’m actually not mainly driven by a desire to live a long time. I accept that when I’m even a hundred years old, let alone older, I may have less enthusiasm for life than I have today. Therefore, what drives me is to put myself (with luck) and others (lots and lots of others) in a position to make that choice, rather than having the choice progressively ripped away from me or them by declining health. Whether the choice to live longer is actually made is not the point for me.
Let’s see 2 possible and extreme interpretations of this answer (neither of them is my own interpretation) and I hope my readers can find fine-tuned arguments in between while thinking a bit about this still rather philosophical topic:
1., Saying that we want the process (a robust healthy lifespan technology) but not necessarily the product (a robust healthy lifespan) of our own business is a disaster Read the rest of this entry »
Posted in Aubrey de Grey, life extension, partial immortalization, philosophy, pimm, SENS | 23 Comments »
Posted by attilacsordas on November 17, 2008
forwarded, nonpersonal mail from Maya Kennard (you might get that email too):
Resource link/Story suggestion for your website:Title: VADLO – Biomedical Search Engine
Description: Vadlo is a search engine for the biology/biomedical scientists, educators, clinicians and reference librarians.
Also check the Daily cartoons!
The idea is that we feed them with searches and links and they will grow big enough to give us more and more relevant searches and links. Magic concept: scalability, check the motivation behind the name choice:
Vadlo: (vud-lo) – Vadlo is a large fig tree characterized by aerial roots that eventually become accessory trunks. This allows it to grow horizontally to amazing proportions.
I find the 5 basic search categories amazing and after a short tinkering it can already throw out interesting sources:
From the about page:
Protocols category will let you search for methods, techniques, assays, procedures, reagent recipes, plasmid maps, etc. Online Tools Read the rest of this entry »
Posted in biology, biotechnology, science, Search Engine, technology | 10 Comments »
Posted by attilacsordas on November 7, 2008
New 23andMe website animation on human prehistory made by Ariana Killoran. Ariana created all the Genetics 101 films for 23andMe and the narrator was her pa. With these films the company clearly sets a new standard in popular scientific animations and videos.
Posted in 23andMe, USA, video | 5 Comments »
Posted by attilacsordas on November 6, 2008
What do you think, which company launched the first commercial and comprehensive personal genome service (based on a genome-wide SNP scan) on the market and exactly when?
We have 2 candidates here in the ring deCODE Genetics (founded in 1996, Iceland) and 23andMe (founded in 2006, USA), the Amundsen and Scott of personal genomics. (please don’t take the analogy too seriously)
The when is important from a historical point of view because that day will be considered as the birthday of this infant industry. The birth month and year is November 2007 for sure. That means we are just approaching the 1 year anniversary of the commercial personal genetics/genomics industry and this sounds like a good timing to think about the achievements so far and the future ahead.
But let’s figure out the exact date first and here I think we should consider the day on which a personal genome service was launched for the first time directly available to costumers and when the first public orders were taken.
Using this measure it seems that the historically first personal genome service Read the rest of this entry »
Posted in 23andMe, biotechnology, deCODE, history, personalized genetics, personalized genomics, science marketing, startup, USA | 12 Comments »
Posted by attilacsordas on November 5, 2008
The newest Nature issue concentrates on personal genomics and its consequences via many types of articles some of them with free access.
I only read 1 piece so far by Erika Check Hayden, who has the exclusive freedom at Nature to always pick the best stories and write on any of them, but being a heavy 23andMe user I was instantly reminded again on the program Promethease with which I can extend the interpretation of my data with an approximately 2 hour run.
According to two commercial gene-testing services — 23andMe and deCODEme — US Army medic Timothy Richard Gall of Fort Belvoir, Virginia, has a higher-than-average risk of basal cell carcinoma, type 2 diabetes and psoriasis. But much more enlightening than these results, which cost Gall more than $1,400, was a free online program called Promethease that he used to further analyse the data. By offering more in-depth information and interpreting of more of his genetic variants, Promethease “gives a much more realistic view of the usefulness of the information”, Gall says. Start-ups and services such as Promethease are now developing ways to improve the limited value of information provided by personal genomics companies for consumers and scientists alike.
Posted in 23andMe, biology, biotechnology, genetics, genomics, journalism, Nature, Nature Publishing Group, personalized genetics, personalized genomics, science, science publishing | 7 Comments »
Posted by attilacsordas on November 5, 2008
A new, completely rewritten, integrated nature.com website blogs.nature.com has been launched by the Natureplex people – informed his Twitter pals Euan Adie:
Also, blogs.nature.com v1 is live! Tequila and donuts all round. Early n’ often release v2 coming on the 18th so get any bug reports in now.
Suggest good science blogs that are not listed on the Nature Blogroll yet.
Posted in blog, Nature, Nature Publishing Group, Natureplex, partial immortalization, pimm, science, science blogs, Twitter, UK | 2 Comments »
Posted by attilacsordas on October 30, 2008
This is a golden day for 23andMe despite all crisis worries:
Mountain View, CA (PRWEB) October 30, 2008 — TIME Magazine announced today that the Personal Genome Service™ from 23andMe, Inc. has been named 2008′s Invention of the Year. 23andMe was chosen as the year’s most significant invention for its exceptional work in making personal genomics accessible and affordable.
From the industrial point of view what are the components of success here besides the obviously good team:
- mission: big, Google-sized mission: revolution of health care by personal genetic information as the source of upcoming personalized medicine
- biotechnology: based on the highest available technology platforms in microarrays (Illumina) (watch out, next gen sequencing is in the corner!)
- capital investment and network effect: I can only repeat myself: 23andMe is probably the most well-connected and backed startup in the history of Silicon Valley.(photo: happy 23andMe founders and early customers)
- information technology the cool and user-friendly factor of the browser based service is really amazing (in the past couple of weeks I demonstrated it to a bunch of people and even those were able to catch the essence of the available information who are older, web-unsavvy)
- simplicity of service: you just spit 2ml into a tube and FedEx it
- most aggressive marketing strategy based largely on the network effect among the power elite of the USA (and consequently, the world)
From the consumer point of view let me tell you 1 personal example of the lifestyle effect of the service: Read the rest of this entry »
Posted in 23andMe, Bay Area, biotechnology, genetics, genomics, google, googleplex, innovation, personalized genetics, personalized genomics, personalized medicine, science, Silicon Valley, technology, US, USA | 6 Comments »
Posted by attilacsordas on October 14, 2008
October 14, 2008 is the world’s first Open Access Day and OA itself means free online access to peer-reviewed research articles. Although we have other, slower methods, like personal homepages, emails to authors, institutional repositories to get the same article we were unable to get via closed access journals, OA is the internet-savvy solution that fits our time and science.
Let me briefly answer question 4 of the synchroblogging initiative: What do you do to support Open Access, and what can others do?
I did a lot of beta testing for free for the upcoming Google Research Datasets in this summer which will host terabytes of scientific raw data that should be in the public domain or have to have a Creative Commons license. I really liked this work.
Here’s what others said on that:
We live in a world where people expect instant, relevant information in the top 20 hits from a Google search and that expectation is transferring to science too. I don’t care how prestigious you think your journal is, or whether you see yourself as some kind of “guardian of knowledge”. I want information, I want it now and if you can’t deliver, I’m going somewhere else.
Neil’s commenter, Stevan Harnad helps clarifying some concepts: Read the rest of this entry »
Posted in open-access, science, science journals, science publishing | 5 Comments »
Posted by attilacsordas on October 9, 2008
The 2009 AAAS Science Dance Contest is for hidden artists disguised as scientists, nerds and shameless self promoters who are tempted to dance their PhDs, upload it to YouTube and enjoy microcelebrity. A real thesis live, non-profit but for fun and a one and only chance to make a fool out of you.
This is a perfect match for John Bohannon, The Gonzo Scientist (whom I introduced you back in 2007) who is an organizer, chronicler and participator of the contest and I must say I liked the rather-theatrical-performance-than-simple-dance version of his thesis, entitled The role of the WSS operon in the adaptive evolution of experimental populations of Pseudomonas flurescens SBW25 (here).
But what to think of the performance of a professor with a thesis title: “Analysis of thymic nurse cells in the chicken”? Artist, nerd, self promoter, did I miss something?
Here are the details of how to enter the contest and don’t miss to read about the prizes too (guests at the 2009 AAAS Annual Meeting in Chicago):
The contest is open to anyone who has (or is pursuing) a Ph.D. in any scientific field, Read the rest of this entry »
Posted in art, culture, nerd, presentation, science, science videos, USA, video, weird | 5 Comments »
Posted by attilacsordas on October 8, 2008
Green fluorescent protein (GFP) is something really familiar for many biologists, now it will be familiar for the whole world for a period via the Chemistry Nobel Prize:
From the Nobel Press Release:
The remarkable brightly glowing green fluorescent protein, GFP, was first observed in the beautiful jellyfish, Aequorea victoria in 1962. Since then, this protein has become one of the most important tools used in contemporary bioscience. With the aid of GFP, researchers have developed ways to watch processes that were previously invisible, such as the development of nerve cells in the brain or how cancer cells spread.
Osamu Shimomura first isolated GFP from Read the rest of this entry »
Posted in biology, Nobel Prize, science | 1 Comment »
Posted by attilacsordas on October 7, 2008
The Google Tech Talks channel on YouTube slowly but irresistibly became my private university in current tech trends. Here is a recent talk on the amazing HealthMap by its developers John Brownstein, Clark Freifeld, Mikaela Keller. According to the about page:
HealthMap brings together disparate data sources to achieve a unified and comprehensive view of the current global state of infectious diseases and their effect on human and animal health.
HealthMap is a Linux/Apache/MySQL/PHP application and relies on the following open products: Google Maps,GoogleMapAPI for PHP, xajax PHP AJAX library, Open Source Web Design
Posted in google, googleplex, medicine, open science, science, technology | 3 Comments »
Posted by attilacsordas on October 5, 2008
It’s Nobel time! Hands up: how many of you have checked so far the official website of the Nobel Foundation called Nobelprize.org? And please try to recall how you usually found out who won the particular Nobel prizes in the past years.
This year the first announcement, for the Nobel Prize in Physiology or Medicine, will be made on 6 October, that is tomorrow. The folks at Nobelprize.org created a list of cool alerts around the Prize Announcements this year and here’s what my inbox detected out of this:
- RSS Feed. Sign up to the 2008 Nobel Prize RSS feed and receive breaking news of the Nobel Prize Announcements and links to exclusive content, such as interviews with the new Nobel Laureates and summaries of the Nobel Prizes, as it appears on Nobelprize.org.
- News Widget. With the news widget , you can discover the names of the 2008 Nobel Prize Laureates on your website, blog or social network. Get the easy-to-add code that will allow you to host the 2008 Nobel Prizes widget.
- iGoogle Gadget. Download the Nobelprize.org iGoogle gadget to discover the identities of the 2008 Nobel Laureates.
- Live Web Casts. All announcements will be broadcast live on Nobelprize.org (except for Peace which is announced in Oslo and for which the video footage will be available after a short delay).
- Twitter alerts. Our Twitter feed lets you keep in touch Read the rest of this entry »
Posted in Nobel Prize, science | 10 Comments »
Posted by attilacsordas on October 3, 2008
Finally 23andMe, my first personal genetics service provider, is on Twitter which could mean that from now on first-hand company information will flow even more continuously compared to what the regularly/daily updated eminent corporate blog can offer. Microblogging is always quicker blogging! Based on the first 4 tweets (on the photo) the guys will not just simply link to the posts but communicate with other Twitterers and give informal & brand new info.
Posted in 23andMe, personalized genetics, personalized genomics, Twitter, USA | 5 Comments »
Posted by attilacsordas on September 28, 2008
I ordered my first commercial genetic profile from 23andMe on the 9th of September online, FedExed my 2 ml saliva from Budapest to 23andMe, Mountain View on the 12th of September. I got the results today. That said within 3 weeks since the birth of the idea I purchased more than 500 000 SNPs of mine analyzed, evaluated and ready to be browsed. With this step I finally and quickly entered into the age of personalized genetics no matter how embryonic it is.
After a superficial first scan of my results I can say that it is a really interesting thing that instantly pushes me towards accumulating more knowledge on the personalized genetics field concerning specific traits, stats, risks and studies.
Here is a first look on what my Y chromosome SNPs are saying on my paternal haplogroup:
I learned for instance that based only on my genotype and not any environmental factors involved I have a lower than average risk Read the rest of this entry »
Posted in 23andMe, biotechnology, Budapest, california, genetics, genomics, partial immortalization, personalized genetics, personalized genomics, science, Silicon Valley, technology, USA | 9 Comments »
Posted by attilacsordas on September 25, 2008
I had problems with my handwriting since elementary schools, or at least my teachers had continuous problems with it. Even during my university years I was asked sometimes to read out loud my essays, papers to them otherwise risking bad grades. Maybe it’s because I am a hidden right-handed using my left hand for writing or maybe I am just too impatient over the slow pace of handwriting (needless to say computers mostly solved this problem).
On this George Dyson photo here you can see the SciFoo schedule in progress and I think you can easily pick the one with the ugliest handwriting on Aging and Life Extension:
Posted in aging, Aubrey de Grey, Chris Patil, google, googleplex, life extension, partial immortalization, personal, science, SciFoo, Silicon Valley, unconference, USA | 7 Comments »
Posted by attilacsordas on September 22, 2008
If you are particularly fascinated by the future and enjoy playing games the following is something you should be involved and interested in. Superstruct, the world’s first massively multiplayer forecasting game started today with Superthreat scenarios by 2019. Game founder Jane McGonigal writes in a message sent to the members of Facebook Group the dedicated to the game:
Watch the news from the future, and find out exactly what dangers and challenges we face with Quarantine, Ravenous, Power Struggle, Outlaw Planet and Generation Exile.
Here is the Outlaw Planet video for instance:
The game is part of The Ten-Year Forecast Program of The Institute for the Future. You can find details in the Superstruct FAQ and as Jessica Hemerly summarizes it:
With Superstruct IFTF introduces a revolutionary new forecasting tool: Massively Multiplayer Forecasting Games (MMFGs). MMFGs are collaborative, open source simulations of a possible future. Each MMFG focuses on a unique set of “future parameters,” which we cull from IFTF’s forecast research. These parameters define a future scenario: a specific combination of transformative events, technologies, discoveries and social phenomenon that are likely to develop in the next 10 to 25 years. We then open up the future to the public, so that players can document their personal reactions to the scenario.
Back in February I participated in a workshop held at Palo Alto where we actually played a Superstruct like game from within the IFTF’s X2 site. Read the rest of this entry »
Posted in future, idea, Superstruct, The Institue For the Future, USA, video | 5 Comments »
Posted by attilacsordas on September 19, 2008
It was already known that amongst the Google top people Sergey Brin is the one who is most interested in pushing biotechnology and the biomedical sciences: in his Stanford years he was interested in biology courses according to The Google Story, he married Anne Wojcicki (who graduted from biology at Yale), Google invested $4.4 million into 23andMe the pioneering personal genomics company co-founded by Anne, then Google invested into 23andMe competitor Navigenics too.
Now Sergey Brin added another, serious and personal reason to think that he is really, personally committed to the quick progress in the biomedical sciences: in his new blog – already a bit of an Internet history – called Too he disclosed that using the 23andMe personal genetics service he figured out something worrying about his and his family’s risk of Parkinson disease (his mother and her aunt are being already diagnosed with PD):
“I learned something very important to me — I carry the G2019S mutation and when my mother checked her account, she saw she carries it too.
The exact implications of this are not entirely clear. Early studies tend to have small samples with various selection biases. Nonetheless it is clear that I have a markedly higher chance of developing Parkinson’s in my lifetime than the average person. In fact, it is somewhere between 20% to 80% depending on the study and how you measure.
The G2019S mutation is actually the rs34637584 SNP and lies in the gene LRRK2 encoding leucine-rich repeat kinase on chromosome 12. The mutation affects the first codon of the gene and is a guanine (G)-to- adenine (A) substitution resulting known as a missense and leads to a glycine – serine (hence the name) amino acid conversion in the protein product. Here is how the SNP position looks in the 23andMe browser using the sample family, the Mendels.
23andMe’s amazingly good corporate blog The Spittoon cited a recent article about the chances: Read the rest of this entry »
Posted in 23andMe, biology, biotechnology, blog, DNA, google, googleplex, life extension, neuroscience, partial immortalization, personalized genetics, personalized genomics, Sci Foo, science, SergeyBrin, Silicon Valley, technology, USA | 14 Comments »
Posted by attilacsordas on September 18, 2008
There is a nice initiative now in Budapest dedicated to the present and future of high technology: a new private university momentarily dubbed as Aquincum Institute of Technology (AIT) will be built near to the Graphisoft Park in Óbuda (Aquincum) concentrating on competitive information-/biotechnology (mainly bioinformatics) education and entrepreneurship.
The main instigator of the project is Gábor Bojár, founder and CEO of the most successful Hungarian software company, Graphisoft.
According to this source:
“The company aims to become the global leader in building-architectural software solutions, hence it must found the training of professionals on a business basis, Bojar said. The new school is to be opened in 2010.”
Mr. Bojár convinced world-class Hungarian scientists and businessmen like Wolf-prize winner discrete mathematician and computer scientist László Lovász, inventor and architecture professor Ernő Rubik, former Office guru, intentional programmer and space tourist Simonyi Charles and scale-free network theorist Albert-László Barabási amongst others to back the idea of a profit-oriented technology university sustained by the market itself.
It’s not too hard to recognize some particular Silicon Valley virtues or models behind the idea of an university like AIT let’s just think about the innovative environment at Stanford, intellectual and entrepreneurial home of the HP, Sun Microsystems and Google founders. What I have in mind here concerning the biotechnology part is The California Institute for Quantitative Biosciences (QB3) which is ‘a cooperative effort between the state of California, the University of California campuses at Berkeley, San Francisco, and Santa Cruz, and industry and venture capital partners’.
The idea can be traced back to a San Francisco dinner Read the rest of this entry »
Posted in bioinformatics, biotechnology, Budapest, business 2.0, education, Hungary, industry, IT, IT&BT, technology | 13 Comments »
Posted by attilacsordas on September 16, 2008
Following Matt Cutts’s tweet I am now writing my blog post using the CrossOver Chromium browser which is a Mac and Linux port of the open source Chromium web browser. Google Chrome (Windows-only so far) is built with open source code from Chromium that means I have now a functional Google Chrome clone under Leopard on my MacBook. This is almost the same experience just like 2 weeks ago. I can use the omnibox, the new home tab and the very clever tab arhictecture amongst others but first of all the browser is now more or less integrated into my customized OS X environment and that is a big advantage. There are of course, inconveniences like crashes and problems with the shortcuts due to the Windows – Mac crossover solutions (which can be modestly modified with Preferences).
Read the rest of this entry »
Posted in Apple, geek, google, googleplex, IT, open source, technology | 13 Comments »
Posted by attilacsordas on September 12, 2008
As the second operation of building my genetically well informed future yesterday (2 days after completing the order) I collected 2 ml of my saliva with the help of 23andMe’s Oragene DNA self-collection kit manufactured by DNA Genotek. First operation has been the sequencing of the D-loop of my mitochondrial DNA out of 5 ml of saliva in the lab at Tulane as a last control experiment, more on that later.
I’d be curious to know approximately how many people in Hungary or in Central Europe, or in all Europe have already used personalized genetics services like 23andMe or the Iceland based deCODE genetics’ genotyping services. As the whole industry is less than 1 year old (starting November 2007) there are not too many public stats available or at least I haven’t found any. With the recent (8th Sep) announcement of the modest $399 kit price reduced from $999 the pioneering personalized genetics service is now affordable for a lot more people, like me (compare it to the $600 iPhone early adopter fee, which I was unable not to buy). Read the rest of this entry »
Posted in 23andMe, biology, biotechnology, Budapest, business 2.0, DNA, marketing, partial immortalization, personalized genetics, personalized genomics, USA | 80 Comments »