LavaAmp: cheapest pocket PCR thermocycler dreamed for DIY biologists

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:

lavaamp-thumb-500x375In 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.

PocketThermocyclerAgrawalpic

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.

Aging-centric genetic health database in California: 100k people, ~65yrs, 700k SNPs, telomeres too

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.

Sage Bionetworks Update: building an OA standard for human disease biology

Sage Bionetworks is a not-for-profit organization developing an open-access “pre-competitive” platform for Sagelogonetworked 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:SagediseasemodelsAnd if that doesn’t sound good enough for a start then the following Sage Datasets will be available in 1 to 2 years: Continue reading

Top 10 PLoS Articles based on online usage

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).

PLoSTopTenArticles

Mapping neurons without glial cells ~ SNP genotyping w/o whole sequencing?

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:

brainmappinganalogy

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.

1st UK Maker Faire, Newcastle, March 2009, makers wanted!

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
innovation.

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. Continue reading

Nature Insight: The complex trait of quantitative genetics

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.

naturequantittivegenetics

Vadlo, the beta biomedical search engine wants to scale up!

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.
References
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:
vadlomitochondria
From the about page:

Protocols category will let you search for methods, techniques, assays, procedures, reagent recipes, plasmid maps, etc. Online Tools Continue reading

Nature Personal Genomics Very Special

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.

naturepersonalgenomes

“blogs.nature.com v1 is live” and beyond

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.

natureblogs

Suggest good science blogs that are not listed on the Nature Blogroll yet.

Golden day for 23andMe: Time’s 2008 Invention of the Year

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: Continue reading

Poll: How will the global economic crisis affect the chances of technological life extension within the next 25 years?

assuming we are heading into a global economic crisis…

For your free information (FYFI): it’s Open Access Day!

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:

Neil Saunders:

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: Continue reading

My body is my thesis: The 2009 AAAS Science Dance Contest

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, Continue reading

Green fluorescent protein wins the Chemistry Nobel Prize!

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 Continue reading

HealthMap & data fusion: detailed Google Tech Talks intro

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

2008 Nobel Prizes on Nobelprize.org: Live webcasts, feeds, Twitter, widgets

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:

Mountain View – Budapest: 20 days to get my 23andMe profile!

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 Continue reading

Science X2 signals: big pharmas, stem cells, mobile MRI

The Institute for the Future‘s X2 project is all about tracing future trends in science and technology As the steward of the Biomedical Sciences and Biotechnology Group I collect signals in these fields on which some forecasts can be based later on. Here are some issues I found future sensitive enough recently:

GlaxoSmithKline collaborates with the Harvard Stem Cell Institute

Pfizer’s growing and various interests in stem cells

Regaining vision with gene therapy using adeno-associated viruses Continue reading

Even ugly handwriting can fit the informal nature of SciFoo

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:

Sergey Brin, Gly2019Ser & a real chance against Parkinson disease/aging!

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: Continue reading

BioBarCamp: we have room for 55 plus Campers!

BioBarCamp is due in circa 3 weeks and we have now 45 BioBarCampers signed up on the list of attendees and our host the Institute For The Future has the capacity for around 55 more campers, roughly for 100 people in general. We already have a very valuable mix: researchers, biologists (grad, postdoc, PI), coders-engineers-bioinformaticians, biotech entrepreneurs, doctors, science journalists.

Here is the list so far and that’s also a chance for you to decide whether you want to join and meet us there in Palo Alto on the 6th and 7th, August and share, ask and answer, be the donor and receptor of ideas from all around biogeekdom. I am continuously trying to collect some links on the campers on the BioBarCamp FriendFeed Room to make future Campers preconnected.

Eva Amsen (writing, blog 1, blog 2)

Michael Andreg

Siamak “Ash” Ashrafi

Monya Baker (Nature Reports Stem Cells, The Niche) 7th, August (added by ACs)

Alex Bangs (Entelos, bio)

Pedro Beltrao (blog, postdoc@UCSF)

Jason Bobe (blog , www.personalgenomes.org, www.DIYbio.org)

Kevin Braithwaite

Martin Brandon

Mackenzie Cowell (diybio.org, pobol, cis-action) Continue reading

Hourglass, a blog carnival devoted to the biology of aging

Finally Chris over at Ouroboros came up with the idea and the quick implementation of Hourglass, a blog carnival devoted to the biology of aging/biogerontology.  For some reason I am not an explicit supporter of blog carnivals – many of my posts were chosen by carnival editors but I never hosted one -, but Hourglass will be the big exception in which I participate, submit posts and host it later. The reason: first it presents aging/biogerontology related posts, which fits my profile and second it was instigated by Chris Patil, whose work is a guarantee for keeping all this in the good direction. So if you want to read on the evolution of longevity and aging, calorie restricition, stem cells/tissue engineering/regenerative medicine, or on the association of long life and intelligence at once, Hourglass is for you.

The decellularized matrix hack: skipping many steps in tissue engineering

The concept of decellularizing complex organs in cadavers and reseeding the remaining matrix structure with differentiated, stem or progenitor cells, growing in a bioreactor and transplanting back to the organism could turn out to be a real technological shortcut in the field of tissue engineering. It is not a brand new story on the web, but it is quite new in science and when I heard Doris Taylor at the Understanding Aging Conference talking on that….well I was really amazed.

Dr. Taylor not only showed the pictures of a complete decellularized rat heart matrix, but in fact they did it on a whole rat framework. So the obvious question is whether the technique could be extended to complete human cadavers (imagine the bone and the bone marrow situation) and if yes, when and how? I am sure if there were a useful clinical near term application of this type of tissue engineering, people would include that option too into their testaments.

And now a pop video on the topic and the abstract:

Perfusion-decellularized matrix: using nature’s platform to engineer a bioartificial heart Continue reading

Understanding Aging Conference is over but it is the end of the beginning

I try to cover some interesting, sciencey points on the conference in later posts, right now just a brief, subjective human- and strategy focused summary:

Congrats to Aubrey de Grey and the team, everything went well and if finally a worldwide consensus is around the corner claiming that robust healthy lifespan extension is technologically possible and worth achieving it is largely due to Aubrey’s relentless networking, organizing activity and American like pushy marketing strategy! Well done!

Had a nice chat with a diverse bunch of interesting people amongst others: Barbara Logan, Nason Schooler, Todd Huffman, Betty Liu, the startupper Andregg brothers, Mark Hamalainen, Keith Causey, Ben Zealley, Brian Martin and sure I forget to mention many more here.

In the photo (thanks Barbara Logan): Neal Van De Ree, Florida auctioneer and activist, John Furber, Legendary Pharmaceuticals, Florida, Aubrey, Paul Logan, Alex Zhavoronkov, GTCBio, BioGerontology Research Foundation Damian Crowe, Genescient, BioGerontology Research Foundation and yours truly.

Conference photo via Bruce Klein: Continue reading

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.

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

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!

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

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

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

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

The Science of Longevity at The World Science Festival, June 1, NYC

90 is the New 50: The Science of Longevity
via Brandon Keim, Wired Science:
Sunday, June 1, 7:00 PM – 8:30 PM,NYU – Kimmel Center for University Life

Will it one day be possible to take a pill to stay young? How will an average life expectancy of beyond a hundred years affect society and the planet? Join leading longevity researchers Robert Butler, David Sinclair and Richard Weindruch to investigate the facts and implications surrounding scientific developments — emerging technologies, novel therapies, and innovative medical practices — that forecast a radical extension of a healthy human life. Featuring a special performance by acclaimed singer, Marilyn Maye.

Tickets: $25.00
Student Tickets: $12.00