Wednesday, November 5, 2008

The DNA Network

The DNA Network

change is coming - but is it all good? [the skeptical alchemist]

Posted: 05 Nov 2008 08:38 PM CST

UPDATE: here is what the status of Prop 8 in California is at the moment (from No on 8).

Nov 05, 2008 Results Status

Roughly 400,000 votes separate yes from no on Prop 8 – out of 10 million votes tallied.

Based on turnout estimates reported yesterday, we expect that there are more than 3 million and possibly as many as 4 million absentee and provisional ballots yet to be counted.

Given that fundamental rights are at stake, we must wait to hear from the Secretary of State tomorrow how many votes are yet to be counted as well as where they are from.

It is clearly a very close election and we monitored the results all evening and this morning.

As of this point, the election is too close to call.

Because Prop 8 involves the sensitive matter of individual rights, we believe it is important to wait until we receive further information about the outcome.

Geoff Kors
Executive Committee NO on Prop 8

Kate KendellExecutive Committee
NO on Prop 8


It is official, it is sealed by the joy of his supporters and the surrender of his opponent: Barack Obama is the new President of the United States of America. "Change is coming to America", he said. But is all of this change necessarily good?

Before you shoot the messenger... I am not talking about Obama's election to the White House. Rather, I am talking about the slew of propositions attached to the presidential ballots, looking to outlaw gay unions in several American states. As of now, the fate of Proposition 8 in California is uncertain, although it looks likely to me that people who just got married might soon enough find themselves to have held empty vows -- not because they are empty per se, but because others have decided so for them.

The current news on Prop 8 are very confusing, but I hope to find out later today what is going on.

In the meantime, here are the two speeches of the year (together with A More Perfect Union, which I am not gonna post here): Obama's acceptance speech, and McCain's graceful speech conceding defeat. I cannot embed them, but you can watch these two high-quality videos just by following the links.

I think once the results for the propositions will be out, and after I have had a few good hours of sleep, it will be time for a reflection -- a reflection about what the consequences of all this will be, what the opportunities, but especially the challenges, now that everyone's expectations are so high -- maybe too high.

It is late now, even on the East Coast. I bid you all a very good night, and I hope you will still follow my ramblings tomorrow, after all the madness will have subsided... good night, and good luck -- for Proposition 8.

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Nature special issue on personal genomics [Genetic Future]

Posted: 05 Nov 2008 07:42 PM CST

In addition to the African and Asian genome studies I discussed in my last post, Nature's latest issue is completely dominated by the topic of personal genomics.

Erika Check Hayden has a nice piece on methods to squeeze the most out of your own personal genomic data, including a profile of the Promethease analysis tool developed by SNPedia's Mike Cariaso and Greg Lennon, which allows personal genomics customers to match their own genetic data against the SNPedia database.

Hayden also gives me my first ever mention in Nature - unfortunately, it's in the context of the unflattering comments I made about the preliminary sequence data released recently by the Personal Genome Project. While I stand by those comments (and I see that PGP leader George Church agrees with them), I do want to note that my criticism was directed purely at the quality of some early-release data, and not at the project as a whole - which I regard as an extremely important step towards the development of personalised medicine, both from a social and a scientific viewpoint. (I should also emphasise that I was expressing my own opinion and in no sense representing the views of my employer, the Wellcome Trust Sanger Institute).

Moving on, Nature also has a fascinating and timely article on the case of the missing heritability - the puzzle of why current genome-wide association studies, despite their well-publicised successes, have failed to uncover the vast majority of heritable disease risk. It's good to see this issue begin to get some serious attention: I've been noting this for a while (see why do genome-wide scans fail?), and David Goldstein raised it in the NY Times back in September, but the vast majority of coverage has focused (perhaps understandably) on the successes of the approach. The article describes several of the places where the missing genetic risk may be hiding, and the challenges of tracking it down - I'll be writing about approaches to tackle a few of these darker regions of the genome (particularly rare variants and copy number variation) over the next month or so.

There's are also articles on the issues of consent in the genome age, and on the troublesome question of what sort of regulation needs to be put in place for the personal genomics industry. These are well worth a read, although I find myself both confused and rather irritated by the latter piece - I guess there's something about the phrase "society should not succumb to fantasies about 'empowered' individuals making free, informed choices in an unregulated genomic marketplace" that just rubs me the wrong way...

Anyway, that's enough rambling from me - go read them for yourself!

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Nature Focuses on Personal Genomics [The Genetic Genealogist]

Posted: 05 Nov 2008 07:00 PM CST

Nature has a brand new web focus on personal genomics (as of November 5th, 2008).  And best of all, most of the articles are entirely free to access, download, and read!  From the site:

“As the number of human beings with their genomes fully sequenced ticks higher and direct-to-consumer gene profiling companies push the limits of what medical genetics can do, the once fantastical notion that any given human can walk into a doctor’s office with his or her genome on a hard drive looks more and more like a reality. Still the question remains to be answered: how do we use this wealth information? In this Nature web focus we proudly present the challenges this approaching reality poses for technology, the legal and ethical confines of research, and the ability of genomics to translate into clinical utility.”

Here are just a few of the interesting news & opinion articles:

And unlike other bloggers who will undoubtedly mention these articles, I recommend that you read or peruse all the articles, not just the ones I happen to agree with!

In addition to the articles, Nature has a podcast (mp3) of special features on personal human genomes.  And lastly, follow along as Nature blogs from the 58th Annual Meeting of the American Society of Human Genetics in Philadelphia from November 11-15.  It looks like this is going to be quite a meeting.

HT: tweet from attilacsordas - are you tweeting yet?  Join me there.

This posting includes an audio/video/photo media file: Download Now

African and Asian genome sequences: the last of the single human genome papers? [Genetic Future]

Posted: 05 Nov 2008 06:30 PM CST


The latest issue of Nature is just as it should be: nearly wall-to-wall human genomics, with a special focus on personal genomics (more on that later).

The main event is a potential historical milestone: quite possibly the last two papers ever to be published in a major journal describing the sequencing of single human genomes from healthy individuals. The papers, which both appear to be open access (kudos to Nature for that decision) describe the analysis of the first Asian genome by researchers at the Beijing Genomics Institute, and the sequencing of the first African genome by a cast of thousands centred around next-gen sequencing company Illumina.

Both genomes were sequenced using next-generation sequencing technology from Illumina, which generates sequence information in the form of very short (35-50 base pair) reads. Although each read is extremely short and relatively error-prone compared to reads from old-fashioned sequencing methods, the sheer number of reads generated by the Illumina technology make whole-genome sequencing feasible: both studies stitched together in excess of 3 billion of these reads to assemble their genomes. That means that each base in the genome was covered, on average, by over 30 independent reads (as opposed to an average of around 7 reads for the Watson and Venter genomes) - more than enough to compensate for the increased error rate of the Illumina platform.

These papers are both important technical achievements, the first of many publications that will emerge over the next few years taking advantage of these short-read technologies to characterise entire human genomes (Watson's genome was also sequenced using next-generation technology, but on a platform that generated much longer reads than the Illumina system at a correspondingly lower throughput). The Illumina platform allows the assembly of an individual genome sequence far more quickly and cheaply than old-school Sanger chemistry, or the 454 platform used for Watson's genome, paving the way for affordable personal genome sequences.

However, many technical challenges still remain. Short read technology struggles to map large insertion/deletion polymorphisms (so-called structural variation), and is almost completely unable to generate accurate sequence data for the 10-15% of the genome that lies in highly repetitive regions. In addition, such platforms are largely unable to determine whether two heterozygous variants are found together on the same copy of a chromosome, or on separate copies (a problem known as phasing). Generating a complete genome sequence in the strictest definition, including accurate phasing, awaits the development of ultra-long read single molecule sequencing platforms.

The papers also illustrate the challenges that lie ahead for personal genomics: an analysis of the Asian genome for potential disease-causing mutations revealed one heterozygous (i.e. single-copy) mutation known to cause deafness, and a possible increase in genetic risk for tobacco addiction and Alzheimer's, but little in the way of convincing, medically actionable results. As I've said before, the technology here is moving much faster than our understanding of the underlying biology - you and I will be able to afford our genome sequences long before we have much idea what they mean.

The other important message from these papers is that we can no longer learn very much in terms of biology from individual genome sequences, at least from healthy people. Each additional genome sequence does contribute a list of new genetic variants, but these returns are rapidly diminishing: in both studies only ~25% of the single-base variants are novel. This proportion is admittedly substantially higher for insertion/deletion and larger structural variants (for which detection approaches are still immature), but that too will diminish with each new genome added to the database and as sequencing technology improves. By the time the 1000 Genomes Project has dumped its last petabyte of data on the web there will be relatively few polymorphisms (variants with a frequency of greater than 1%) left to discover, at least in the European, East Asian and West African populations.

So attention has already well and truly turned to converting sequence into biological meaning - and that's a job that will ultimately require many hundreds of thousands of genome sequences, each attached to information about biological traits and disease status. That means the end of the brief era of high-profile "single human genome" papers, which started in a sense with the anonymised, pooled and fragmented human reference sequences published in 2001, peaked with the celebrity genomes of Venter and Watson in 2007/2008, and now ends (I suspect) with two anonymous non-European genomes.

Of course, we will still see a number of papers describing whole genomes of diseased individuals, particularly tumour samples - indeed, there is one such paper in the same issue of Nature, which you can read about at PolITiGenomics.

But nonetheless, the age of the one-genome paper is fast drawing to a close. Human genetics now moves into a phase of new challenges and rewards - the era of population genomics.

Subscribe to Genetic Future.

Wang et al. (2008). The diploid genome sequence of an Asian individual Nature, 456 (7218), 60-65 DOI: 10.1038/nature07484

Bentley et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry Nature, 456 (7218), 53-59 DOI: 10.1038/nature07517

Images of average East Asian and African faces from Face Research.

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Post-admixture selection among Mexican Americans? [Yann Klimentidis' Weblog]

Posted: 05 Nov 2008 05:22 PM CST

This paper examines the variation in admixture proportions across the genome at 284 microsatellite markers among 392 Mexican Americans. They find increased European ancestry on a region of chromosome 1, and decreased African ancestry on Chromosomes 2 and 9 (see figure on right: "Genome-wide distribution of African (bottom line), European (top line) and Native American (middle line) ancestry. The dashed vertical lines correspond to chromosome boundaries. Chromosomes are listed in numerical order from 1 to 22")
Since the markers are widely spaced out, they couldn't pinpoint any specific genes. Interestingly, these results differ pretty dramatically compared to a previous similar study among Puerto Ricans. Also, interestingly, since they had people who were hypertensive or had diabetes, and people who didn't, they were able to determine that the identified regions were not associated with these health outcomes, since the local ancestry at those areas was no different between cases and controls.
They do make some mention at the end that they might expect selection at infectious-disease related genes given that the ancestral parental populations that had adapted to specific environments were suddenly faced with different environments.

Genome-wide distribution of ancestry in Mexican Americans
Analabha Basu, Hua Tang, Xiaofeng Zhu, C. Charles Gu, Craig Hanis, Eric Boerwinkle and Neil Risch
Human Genetics Volume 124, Number 3 / October, 2008
Abstract Migrations to the new world brought together individuals from Europe, Africa and the Americans. Inter-mating between these migrant and indigenous populations led to the subsequent formation of new admixed populations, such as African and Latino Americans. These unprecedented events brought together genomes that had evolved independently on different continents for tens of thousands of years and presented new environmental challenges for the indigenous and migrant populations, as well as their offspring. These circumstances provided novel opportunities for natural selection to occur that could be reflected in deviations at specific locations from the genome-wide ancestry distribution. Here we present an analysis examining European, Native American and African ancestry based on 284 microsatellite markers in a study of Mexican Americans from the Family Blood Pressure Program. We identified two genomic regions where there was a significant decrement in African ancestry (at 2p25.1, p less than 10−8 and 9p24.1, p less than 2 × 10−5) and one region with a significant increase in European ancestry (at 1p33, p less than 2 × 10−5). These locations may harbor genes that have been subjected to natural selection after the ancestral mixing giving rise to Mexicans.

What Our Genes Tell Us About Race [adaptivecomplexity's blog]

Posted: 05 Nov 2008 04:50 PM CST

Which species is more diverse, humans or chimps? Most of us would be tempted to answer 'humans'. Unless you're a primatologist or you work at a zoo, you would likely have trouble telling one chimp apart from another, not to mention distinguishing between West African and Central African chimpanzees. By contrast, we can easily spot differences among humans - if asked to guess whether someone was from China, Pakistan, or Kenya, few of us would have any trouble getting the answer correct.

By the measure of genes though, humans are amazingly uniform. Humans are genetically less diverse than chimps, and both chimps and humans are much less diverse than a common species of fruit fly. Given our species' long history of racial conflict, our genetic uniformity may come as a surprise. Not too long ago people in polite company would debate whether different human races really all belonged to one species. Our DNA tells us that our genetic differences don't even come close to matching the variety found within a single, apparently monotonous fruit fly species.

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Blogging from Bangladesh [Tomorrow's Table]

Posted: 05 Nov 2008 04:10 PM CST

The posts this week will be from Bangladesh and India. I have temporarily moved the blog to

Nature network

Economic Woes Hit the Academic Job Circuit [The Daily Transcript]

Posted: 05 Nov 2008 04:05 PM CST

From confidential sources I have heard of at least two academic institutions, one in the Boston area and one on the West Coast, that have canceled their new faculty searches due to the current financial crisis. How widespread is the problem? We'll have to wait and see.

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Claiming my blog on the new Nature Blogs. [Synthesis]

Posted: 05 Nov 2008 12:31 PM CST

Cloning extinct species, and Michael Crichton won't be here to see it [Mary Meets Dolly]

Posted: 05 Nov 2008 12:30 PM CST

(AP Photo/Jim Cooper, file)
Today is truly a sad day for me.  Not simply because the pro-death agenda has won in nearly every major arena in this country, but because Michael Crichton died yesterday of cancer.

As a young person, Jurassic Park and the Andromeda Strain not only presented science to me in an interesting way, but along with a great story were ethical concerns regarding what scientists should and should not do.  More recently, NEXT exposed the possibilities and the horrors of where genetic engineering will take us and The State of Fear introduced us to the dangers of science as a kind of religion.

Michael Crichton knew ethics and science had to go hand in hand.  He presented to the average person the idea that science gone amok was not something we ever wanted to experience.

I think it is ironic that Japanese researchers have announced that they have successfully cloned mice using cells from a mouse frozen for 16 years.  Now there is talk of attempting to clone the Mammoth, extinct for thousands of years. 

Jurassic Park has come to real life and Michael Crichton, the man who introduced the world to the possibilties of cloning extinct species, will not be alive to see it.  I already miss the books he never got to write.

I pray for Michael Crichton and his family.  And to take my mind off the depressing elections results, I think I am going to read The Great Train Robbery again.

Genetic Test or Family History? Which Matters More? [The Gene Sherpa: Personalized Medicine and You]

Posted: 05 Nov 2008 11:12 AM CST

I would say that when used in combination a 3 generation family history and appropriate genetic testing are probably the best tools we have to identify risk for and diagnose genetically linked...

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Get Your Bio-Imagination On []

Posted: 05 Nov 2008 10:38 AM CST


Nothing like a little speculative fiction to keep you interested in the potentials of new technology. Biotech has a whole genre dedicated to the ever-expanding “what-if” scenarios: Biopunk, defined as “a sub-genre of cyberpunk fiction that portrays the underground side of the ‘biotech revolution’ which, in the 1990s and 2000s, was expected to start having a profound impact on humanity in the first half of the 21st century.”


We recently stumbled across an entry on the blog Enter The Octopus entitled, “Toward a list of essential readings in biopunk fiction” that serves as a pretty great starting point for the intrigued. Aminopop says check it out.

Metagenomics 2008 Meeting Notes [The Tree of Life]

Posted: 05 Nov 2008 10:31 AM CST

I am going to post notes here for the Metagenomics 2008 meeting.

#1 - most everyone here seems really happy about the election

#2 - mooched a ride this morning to the conference site from some of the folks who run "The Seed" and related annotation and analysis servers.  I have written about them before but people really should check them out if you are interested in microbial genome analysis. 

#3 - Alex Worden is talking now about picoeukaryotes.  Alex does some of the coolest environmental microbiology out there and just happens to focus on groups of organisms that are frequently ignored.  She just said a key quote "Physiology is not a bulk or an average property" basically saying what I say which is that an environment is not simply a bag of genes.  That is we need to remember that there are real compartments in communities.  Alex just showed an interesting figure on rRNA sampling of uncultured eukaryotes from the Sargasso See (Not et al. EM 2007).   Another key point she has made is that microbial eukaryotes are barely sampled in terms of genomics

#4 - a ridiculously short break (the organizers of this meeting really really need to change the scheduling to have more time to talk to people in breaks).  

#5 - Oded Beja is talking now.  He is really one of the key people behind the entire metagenomics revolution as he was the lead on many of the papers from the Delong Lab onthe discovery of proteorhodopsin

#6 - Shannon Williamson is showing an incredibly cool contraption that she uses to take water samples and size fractionate them in the bottom of the ocean.  It is basically a series of filter systems that works on a platform that is run by a deep sea submersible ... this allows them to sample large volumes of water in the deep sea (larger volumes than they could bring back up to the surface)

#7 - a little note --- already many talks referring to using IMG, IMG/M and MG-RAST tools to help with annotation and analysis of genomes and metagenomes.  Clearly there is enormous demand for getting ones data analyzed by some public or semi-public tools ...

#8 - Yuri Gorby --- gave a talk about nanowires which are basically little mini cables that cells use to connect to other cells and shuttle electrons around.  This stuff is beyond cool --- it is completely fascinating.

Family History of Disease Scares Parents More Than Genetic Test Results [Eye on DNA]

Posted: 05 Nov 2008 10:05 AM CST

image Should parents purchase direct-to-consumer genetic tests for their under-age children? Joanna Mountain, Senior Director of Research at 23andMe, chose to do so for her two sons and found it to be a positive experience overall (of course!). I have not done so for my two children and haven’t even done so for myself. Just call me chicken.

In a timely study published in the November issue of the Archives of Pediatrics & Adolescent Medicine, researchers at the University of Michigan CS Mott Children’s Hospital staged a hypothetical situation and randomized over 1,300 parents to receive hypothetical genetic risk assessments framed as family history or genetic test results. They found that parents were actually more worried if they had observable, tangible evidence of a family history of disease than if the results were purely based on genetic tests.

So it seems that nothing strikes fear into our hearts more than knowing that a family member is ill and that we may also have inherited an increased susceptibility to the illness. While genes may be floating around in our consciousness, they remain an abstract concept that most of us are not able to include in our daily risk analyses.

NB: Daniel MacArthur at Genetic Future has more on genome scans for the whole family although he considers it mainly from a business perspective than from one as a parents since he isn’t one yet.

via Los Angeles Times

Photo credit: Wellcome Images

The Morning After [The Daily Transcript]

Posted: 05 Nov 2008 07:50 AM CST

Just like a giant, well controlled, negative result right wing ideology has been repudiated. If I were a card-carrying member of the GOP, I would take a long look at the last 8 years, and a hard look at the demographics of this election. I won't reiterate my displeasure of libertarian fundamentalism with respect to the market, instead we'll be looking at what happened yesterday. Here are some eye popping numbers for you:

In 2050 more than 50% of American will be a member of a racial minority group, be it Hispanic, Black or Asian. So how did they vote?
Black: 95% Obama, 4% McCain
Hispanic: 66%, 31%
Asian: 62%, 35%

And for Joe the Plumber who spouted this nonesense that a vote for Obama is a vote for the death of Israel
Jews: 77% Obama, 22% McCain

If I were a Repulican, I would look to see how I am doing with the next generation of voters. But it doesn't look good.
First Time Voters: 69% Obama, 30% McCain
18-29 year olds: 66% Obama, 31% McCain

Here is the data of Age vs Republican Vote % from the past few elections (from Red State Blue State)


And finally in Massachusetts Proposition 1, which would have banned income tax was soundly defeated 70% to 30%

The only dissapointments were a few propositions of note in California.
- Proposition 8, a constitutional ban on same sex marriage passed.
- Proposition 10, money for alternative fuel vehicles and renewable energy failled, however this was partially compensated with the passing of Proposition 1, which provides money for a high speed train.

Data from NYTimes' Election Results

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Social Media for Scientists [Sciencebase Science Blog]

Posted: 05 Nov 2008 07:01 AM CST

social-media-for-scientistsTowards the end of October, I received a flurry of emails asking me to check out new social networking sites for scientists, I’ve already reviewed the nanoscience community, of course. I suspect that, the academic year having moved into full swing, there were a few scientists hoping to tap into the power of social media tools and the whole web-two-point-ohhhh thing.

This from Brian Krueger:

“I came across your blog during my weekly google search for “science social network.” I thought you might be interested in my website, It’s a social network for the sciences that I’ve had on-line for the last two years and I recently got my University to send out a press release about it. I think you should stop by and check it out. Let me know what you think, I’m always looking for suggestions on how to improve the site.”

LabSpaces has all of the features of a social-networking site with the addition of a daily science newsfeed, lab profiles, a science forum, blogs, and a science protocol database. Apparently, the site provides space for researchers to create their own user profile, add their publication history, upload technical research protocols, blog about science, and share research articles with the community. The site will soon host a free video conferencing service to facilitate long distance collaborations and journal clubs.

New Zealander Peter Matthews who works in Japan emailed:

“I am a full-time researcher from NZ, working in Japan, at a museum with many international research visitors. This multilingual environment made me very aware of: (1) the difficulties that non-English based researchers face when using English, and (2) the difficulties that English mono-linguals face when trying to access or publish research in other important research languages, such as Spanish, Chinese, Japanese, French, and so on. Hence my website: The Research Cooperative - Please have a look, join if you want, and please tell any friends and colleagues about this site if you think they might find it useful.”

Pascal Boels, Managing Director of emailed with a medical tale:

“Our website is for and by medical professionals. It's a video-sharing site for surgeons and medical professionals to show off their newly minted skills. It makes it easy for medical professionals to upload videos or slideshows and share those with the community. You can search for videos by specialty, organ/region, tissue, etiology, operation type, or technique. Many surgeons perform original and high-quality techniques in their operating room and equally many surgeons would like to learn from these new and inspiring techniques. Up till now it was very difficult, time consuming and expensive to take a look in each others operating room and share practical knowledge, tips and tricks. provides the solution for this problem. We are currently serving over 4000 surgeons from more than 124 countries, sharing over 400 procedures

Priyan Weerappuli had long been interested in scientific research but felt that applied research was guarded by private institutions while basic research was held within the confines of colleges and universities by overpriced journals and an oversimplification that occurred whenever research results were translated for more general audiences. His forum/platform will attempt to open this research to a general audience -

Some correspondents are claiming they’re approaching web 3.0 nirvana:

“ResearchGATE is proud to announce a major update: We greatly improved our search functionality and called it ReFind. The name symbolizes the importance of an efficient and result-driven search functionality within research in general and within our network in particular. ReFind is one of the first search engines based on semantic, “intelligent” correlations. It enables you to find groups, papers, fellow researchers and everything else within and outside of ResearchGATE without having to read through dozens of irrelevant results. Just type a few sentences into ReFind or simply copy and paste your abstract. Our semantic algorithm will then search the leading databases for similar work, providing you with truly relevant results.” [Sounds like my Zemanta/ idea, DB]

One observer pointed out, however, that ResearchGate’s semantic search is maybe not the greatest thing to happen to search in a decade (especially, when we have the likes of True Knowledge Ubiquity, and Zemanta. Indeed, some users have said it is not much of an improvement on conventional search.

Then there was:

“ - Science in the 21st century - A wide forum for science - on an interdisciplinary, international and individual level., the only universal online portal for science, advanced teaching and academic research, bridges a major gap in scientific research and learning. is a virtual conference room, lecture hall, laboratory, library and meeting venue all in one.”

But, perhaps the best is saved for last. An Oxford graduate student, who has completed his PhD, Richard Price, has launched, which he says does two things:

“It displays academics around the world in a ‘tree’ format, according to which institution/department they are affiliated with. And, it enables researchers to keep track of the latest developments in their
field - the latest people, papers, and talks.”

Price wants to see every academic in the world on his tree and already has Richard Dawkins, Stephen Hawking, Paul Krugman, and Noam Chomsky as members. But, that’s the hype what about its potential? It resembles BioMedExperts because both use a “social” publishing tree, but is that enough to engage scientists?

It will be interesting to see whether any of these sites gain the traction their creators hope for and how things will pan out as the credit crunch bites harder. “There are a bunch of them out there,” Krueger told me, “It’s kind of scary how many came out after Nature and I went on-line in 2006. There’s definitely a lot of competition out there, it seems like a new one appears every month. I wonder how the economy and loss of tech funding is going to affect the larger start-ups.”
Then, there are those perhaps more well-known social media sites and networks for scientists, some of which are mentioned in Sciencebase and its sibling sites (tomorrow), in no particular order:

There are so many, I can barely keep up, but if you have any you think I should add to the list, let me know via the comments box below. Or, more importantly, if you have used any of these systems please leave your thoughts.

Meanwhile, my apologies if you were expecting a lesson in how to use the likes of Twotter, FiendFreed, Ding, Pyuke, or Facebok’s feeble science apps, to help you get on in science socially, but I thought it was about time I did some linking out to the web 3.0 brigade in the world of science, so here they are.

Social Media for Scientists

President Obama and the Genome [The Gene Sherpa: Personalized Medicine and You]

Posted: 05 Nov 2008 06:18 AM CST

Now that we have a new president many may wonder what will occur in the realm of personalized medicine. Well, the short answer is ALOT. Several things that the democratic majority in the house,...

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Metagenomics Meeting --- Competing with the Election [The Tree of Life]

Posted: 05 Nov 2008 12:29 AM CST

Well, I apologize but I am not going to post anything today about the metagenomics meeting in San Diego since I came late today as I wanted to be at home for the beginning of the election.  But I made my way down to San Diego and made it to dinner.  The dinner "entertainment" was a talk by one of the grand gurus of ocean microbiology - Steven Giovannoni.  Alas, even he realized that he was competing with people wanting to know about the election and I confess I spent most of his talk hitting reload on my phone and surfing between sites.  So I have no notes to post about his talk.  But I can say that I am happy about the election.  And tomorrow I will try to post some notes about talks.  But I may be still too happy to take notes ...

Research Funding: Low Hanging Fruit [Bayblab]

Posted: 04 Nov 2008 11:18 PM CST

A few weeks ago, Bayman posted a story from the Globe and Mail about unrealistic expectations for a cure for cancer and in the comments AC wrote
I think the expectation comes from the fact that we've basically cured many diseases that were low-hanging fruits [...] And it might or might not be worth the money; perhaps we could cure 100 smaller diseases for that price.
It turns out that focus on low-hanging fruit is also an issue within the cancer research community. The Independent reports that in spite of record levels of funding for cancer research in the UK many "unfashionable" cancers are being neglected:
Some of the deadliest cancers, such as those affecting the lung and pancreas, get the least amount of public money, while five cancers with some of the best survival rates, including breast and leukaemia, receive nearly two-thirds of the money.
This seems counterintuitive. One would think that cancers such as lung cancer - which remains the leading cause of cancer death for both men and women - would receive a higher percentage of funding dollars. But that isn't the case. This is attributed to the fact that current research focuses on areas where major discoveries are more likely or the disease is easier to study, and this is partly due to the fact that future grants can depend on past success so reaching for those higher fruits can be risky career-wise. Is this a problem? Should focus shift from areas with diminishing returns to those where there's still a lot of ground to be covered? Or should we finish off the 'low hanging fruit' before climbing the ladder? And if the former, how do we accomplish it?

Congratulations Mr. Obama! [Discovering Biology in a Digital World]

Posted: 04 Nov 2008 10:50 PM CST

There are tears of joy and relief in my eyes. It's like the most emotional New Year's Eve in my life.

My neighbors are even shooting off fireworks!

Mr. McCain's speech was wonderful. Let's move forward!

Update: I am watching Mr. Obama now on TV with tears in my eyes. I have never been so glad to be an American.

Yes we can, Mr. Obama, yes we can!

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More about How I feel - from my iPhone [The Tree of Life]

Posted: 04 Nov 2008 10:22 PM CST

How I feel - drawn on my iPhone [The Tree of Life]

Posted: 04 Nov 2008 10:18 PM CST

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