by oskay
15 human genomes each week:
[Via Eureka! Science News - Popular science news]

The Wellcome Trust Sanger Institute has sequenced the equivalent of 300 human genomes in just over six months. The Institute has just reached the staggering total of 1,000,000,000,000 letters of genetic code that will be read by researchers worldwide, helping them to understand the role of genes in health and disease. Scientists will be able to answer questions unthinkable even a few years ago and human medical genetics will be transformed.
[More]

Some of this is part of the 1000 Genomes Project, an effort to sequence that many human genomes. This will allow us to gain a tremendous amount of insight into just what it is that makes each of us different or the same.

All this PR really states is that they are now capable of sequencing about 45 billion base pairs of DNA a day. They are not directly applying all of that capability to the human genome. While they, or someone, possibly could, the groups involved with 1000 genomes will take a more statistical approach to speed things up and lower costs.

It starts with in depth sequencing of a couple of nuclear families (about 6 people). This will be high resolution sequencing equivalent to 20 passes of the entire genome of each. This level of redundancy will help edit out any sequencing errors from the techniques themselves. All these approaches will help the researchers get a better handle on the most optimal processes to use.

They were hoping to be sequencing the equivalent of 2 human genomes a day and they are not too far off of that mark. At the end of this study, they will have sequenced and deposited into databases 6 trillion bases (a 6 followed by 12 zeroes). In December 2007, GenBank, the largest American database had a total of 84 billion bases (84 followed by 9 zeroes) that took 25 years to produce.

And, more importantly, the scientists doing the examining will have to appreciate the sheer size of this. It took 13 years to complete the Human Genome Project. Now, 5 years after that project was completed, we can potentially sequence a single human genome in half a day.

The NIH had projected that technology will support sequencing a single human genome in 1 day for under $1000 in 4 years or so. The members of 1000 genomes are hoping to be able to accomplish their work for $30-50,000 per genome. So, the NIH projection may not be too far off.

Maybe I should invest in data storage companies.

Technorati Tags: Health, Science

Life Sciences likes this: Friendfeed:
[Via OpenWetWare]

I’m going to assume that only those currently using FriendFeed will understand the self reference in the title but if you didn’t that’s OK. Just keep on reading, you’ll get it, eventually.

If you happen to be interested or work in the life sciences area I’d recommend you take a few minutes to read Cameron Neylon’s great post about FriendFeed and how it’s been embraced by the life sciences community.

I won’t go into the details of how FriendFeed works, but it’s been rapidly gaining momentum as a medium for groups of users to network and discuss each other’s shared content.

FriendFeed’s about page states:

FriendFeed enables you to keep up-to-date on the web pages, photos, videos and music that your friends and family are sharing. It offers a unique way to discover and discuss information among friends

The life sciences community has picked up on this great website like wildfire. A recently created room called The Life Scientists grew in a very short period (a week?) from just a few active online colleagues to a whooping 100+ users.

FriendFeed rooms offer a way to share on-topic content and further discussion via comments. Commenting can be done on any shared items (yours or others). This has proven to be useful for rapid input and idea sharing amongst the room’s users.

Amongst the 100+ users of the Life Scientists room, both Cameron from Science in the Open and Pedro from Public Rambling have found FriendFeed to be useful and explain why it works. Both great reads.

This is the sort of tool that can very rapidly connect researchers, in ways that Twitter or Facebook do not. Not only can links be put up rapidly but comments are there very fast. It allows one to ask questions, post answers. It is a lot like how the Bionet newsgroup, which you can still access, used to be back in the old days (i.e. 1993-95) when Usenet ruled the Internet.

This is the online equivalent of the water cooler where you can run into someone and strike up a conversation that could lead to innovative thinking. Only instead of two people having to occupy the same space at the same time, this approach decouples both, permitting a much wider circle of people to be involved.

Technorati Tags: Knowledge Creation, Social media, Web 2.0

from Alexander Rich

Kevin Kelly — The Technium:
[Via The Technium]

Scenius is like genius, only embedded in a scene rather than in genes. Brian Eno suggested the word to convey the extreme creativity that groups, places or “scenes” can occasionally generate. His actual definition is: “Scenius stands for the intelligence and the intuition of a whole cultural scene. It is the communal form of the concept of the genius.”

Individuals immersed in a productive scenius will blossom and produce their best work. When buoyed by scenius, you act like genius. Your like-minded peers, and the entire environment inspire you.

The geography of scenius is nurtured by several factors:

Mutual appreciation — Risky moves are applauded by the group, subtlety is appreciated, and friendly competition goads the shy. Scenius can be thought of as the best of peer pressure.
Rapid exchange of tools and techniques — As soon as something is invented, it is flaunted and then shared. Ideas flow quickly because they are flowing inside a common language and sensibility.
Network effects of success — When a record is broken, a hit happens, or breakthrough erupts, the success is claimed by the entire scene. This empowers the scene to further success.
Local tolerance for the novelties — The local “outside” does not push back too hard against the transgressions of the scene. The renegades and mavericks are protected by this buffer zone.

Scenius can erupt almost anywhere, and at different scales: in a corner of a company, in a neighborhood, or in an entire region.
[More]

Kevin discusses a specific instance of scenius but the idea is something that needs greater examination. Because innovation, creativity and new insights rarely if ever happen because of a single person in isolation. They happen in a social network made up of the right mix of people to allow innovation to blossom. However, an important aspect, especially today, is that the scene for this genius does not need to occupy the same space. The specific network can be made up of people physically separated.

Now this great discovery was noticed by a pre-eminent physicist, George Gamow, who, to my mind, is one of the great scientists of the 20th century, not only for his own work but for his impact on other scientists. Here is how Wikipedia starts his entry:

George Gamow (pronounced as IPA: [ˈgamof]) (March 4, 1904 – August 19, 1968) , born Georgiy Antonovich Gamov (Георгий Антонович Гамов), was a Russian Empire-born theoretical physicist and cosmologist. He discovered alpha decay via quantum tunneling and worked on radioactive decay of the atomic nucleus, star formation, stellar nucleosynthesis, big bang nucleosynthesis, nucleocosmogenesis and genetics.

Nice, wide ranging scientific career. Look at his accomplishments (again from Wikipedia):

Gamow produced an important cosmogony paper with his student Ralph Alpher, which was published as “The Origin of Chemical Elements” (Physical Review, April 1, 1948). This paper became known as the Alpher-Bethe-Gamow theory. (Gamow had added the name of Hans Bethe, listed on the article as “H. Bethe, Cornell University, Ithaca, New York” (who had not had any role in the paper) to make a pun on the first three letters of the Greek alphabet, alpha beta gamma.)

The paper outlined how the present levels of hydrogen and helium in the universe (which are thought to make up over 99% of all matter) could be largely explained by reactions that occurred during the “big bang“. This lent theoretical support to the big bang theory, although it did not explain the presence of elements heavier than helium (this was done later by Fred Hoyle).

In the paper, Gamow made an estimate of the strength of residual cosmic microwave background radiation (CMB). He predicted that the afterglow of big bang would have cooled down after billions of years, filling the universe with a radiation five degrees above absolute zero.

Gamow published another paper in the British journal Nature later in 1948, in which he developed equations for the mass and radius of a primordial galaxy (which typically contains about one hundred billion stars, each with a mass comparable with that of the sun).

Astronomers and scientists did not make any effort to detect this background radiation at that time, due to both a lack of interest and the immaturity of microwave observation. Consequently, Gamow’s prediction in support of the big bang was not substantiated until 1964, when Arno Penzias and Robert Wilson made the accidental discovery for which they were awarded the Nobel Prize in physics in 1978. Their work determined that the universe’s background radiation was 2.7 degrees above absolute zero, just 2.3 degrees lower than Gamow’s 1948 prediction.

I have to love any genius who authors a paper that makes such a great pun. Some of the best geniuses are great tricksters (Feynman loved to pick locks or break combination safes.)

But my story is not about Gamow and the big Bang theory. I’ll let this, from Nobelprize.org, discussing the breaking of the genetic code, provide some context for Gamow’s genius, and how he created a scenius that spanned continents:

When the structure of DNA was made known, many scientists were eager to read the message hidden in it. One was the Russian physicist George Gamow. Many researchers are ”lone rangers” but Gamow believed that the best way to move forward was through a joint effort, where scientists from different fields shared their ideas and results. In 1954, he founded the “RNA Tie Club.” Its aim was “to solve the riddle of the RNA structure and to understand how it built proteins.”

The brotherhood consisted of 20 regular members (one for each amino-acid), and four honorary members (one for each nucleotide in nucleic acid). The members all got woolen neckties, with an embroided green-and-yellow helix (idea and design by Gamow).

Among the members were many prominent scientists, eight of whom were or became Nobel Laureates. Such examples are James Watson, who in the club received the code PRO for the amino acid proline, Francis Crick (TYR for tyrosine) and Sydney Brenner (VAL for valine). Brenner was awarded the Nobel Prize in Physiology or Medicine as recently as 2002, for his discoveries concerning genetic regulation of organ development and programmed cell death.

Early Ideas Sprung from the “RNA Tie Club”

The members of the club met twice a year, and in the meantime they wrote each other letters where they put forward speculative new ideas, which were not yet ripe enough to be published in scientific journals.

In 1955 Francis Crick proposed his “Adapter Hypothesis,” which suggested that some (so far unknown) structure carried the amino acids and put them in the order corresponding to the sequence in the nucleic acid strand.

Gamow, on the other hand, used mathematics to establish the number of nucleotides that should be necessary to make up the code for one amino acid. He postulated that a three-letter nucleotide code would be enough to define all 20 amino acids.

Eight out of 20 won Nobel prizes (although there is some humorous ways to look at this that give better clues on how this was accomplished). Not very bad odds. Much like Kelly’s mountain climbers. The scenius attracts, nourishes and sprouts geniuses. But it is the first scientific scenius I am aware of that was not tethered to a single location and some very critical things came up from these interactions. For instance, Crick delineated the 20 amino acids used to make up proteins as an intellectual exercise, written on a pub napkin. He was right.

This group worked a lot to try and figure out how RNA made protein, thus the name RNA Tie Club (Gamow made sure each had an appropriate tie for their amino acid). There were many informal and speculative papers that they wrote to each other (remember that this was a time where biology and genetics were mainly descriptive. Speculation and deductive approaches to biology were not commonly used.) Many of these approaches were flat out wrong. But these errors allowed them to eventually gain some wisdom.

Some of the papers have become parts of biology lore, because the speculations turned out to be correct and led to really important breakthroughs in the field. Here is the most important one, Francis Crick and his Adaptor hypothesis, the paper for the RNA Tie Club that developed tRNA and a degenerate genetic code as a model. On Degenerate Templates and the Adaptor Hypothesis is one of the most famous unpublished papers I know of.

To get some idea of how this all worked, check out Watson’s response to Crick Adaptor paper for the RNA Tie Club. Watson was at CalTech at the time.

Gamow. was here for 4 days - rather exhausting as I do not live on Whiskey. Your TIECLUB note arrived during visit. Am not so pessimistic. Dislike adaptors. We must find RNA structure before we give up and return to viscosity and bird watching.

Being able to create and foster such a scenius will be an important part of many organizations.

Technorati Tags: Biology, Science, Web 2.0

You know the conference you are at is too big when ….:
[Via The Tree of Life]

You know the conference you are at is too big when ….

Now - I confess I was really impressed with how ASM handled this enormous meeting I was just at. If you are going to have a big meeting, ASM does a smashing job. And I can see how such big meetings can have their appeal - the diversity of work and activities relating to Microbiology are amazing. However, big meetings are still not my cup of tea.

So here is my top 10 list of “You know the conference you are is too big when …”. All are based on experiences from this meeting.

1. People communicate within the conference venue by email and cell phones
2. They give you a foldout map showing the locations of all the different venues/activities/
3. Colleagues contact you electronically after your talk rather than in person
4. The lines for food are longer than the lines for security at the airport
5. There are more:
• counters at the registration booth than at the airport ticket area
• meeting staff than scientists at the last conference you attended
• promotional booths than active players in Major League Baseball (OK, we are not quite there with this meeting but we are close)
6. The abstract book weighs more than your laptop computer
7. People use GPS to find their way in the conference center (I wish I had pictures but I saw this happening)
8. The bus/shuttle scheduling system is more complex than the travelling salesman problem
9. You need to plan your own schedule by searching a database
10. You do more walking inside the conference center than outside

I have had to deal with every one of these at big conferences. Many of the points hit one of the big drawbacks from mammoth conferences - they depersonalize the experience.

Big conferences often give me little reason to attend. Their massive size is disconcerting. It is harder to find a hotel or restaurant. The social interactions are diminished. Why take the effort?

Technorati Tags: Science

by ul_Marga

There is a possibly interesting paper in Genome Biology by Barend Mons et al: Calling on a million minds for community annotation in WikiProteins. I say possibly because the paper itself is quite confusing to me but the overall goal seems to be a cool concept. This group has created and is encouraging the use of “WikiProteins” a community annotation system for “community knowledge.” Sounds a bit fuzzy? Well, reading the paper does not completely help. For example here is the abstract

WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a ‘million minds’ to annotate a ‘million concepts’ and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org webcite.

[More]

This is an interesting attempt but the community they are asking for is not in existence yet. The goal is extremely worthwhile, since the best way to create knowledge from the huge mountain of data being created is to incorporate large social networks. But the community must be created first.

However, at the moment in the science community there is a large activation energy (yes, human social interactions also require energy to be expended in creating the network before the information flow can become self-sustaining). First, there needs to be demonstrable proof that putting time into community annotation will be productive and rewarding. There is no proof of this yet.

Online communities will be how we solve the difficult problems facing us. The sooner they are functional, the sooner we can begin finding solutions.

Technorati Tags: Science, Web 2.0

independentman
Getting Conversation Ready:

[Via Beth's Blog: How Nonprofits Can Use Social Media]

Holly Ross wrote a good reflection piece about public conversations on blogs and how to get your audience ready for that conversation. She makes the point:

What I am saying is that your audience may not be ready to have the conversation that social media enables. That’s because social media does not just enable conversations.It enables PUBLIC conversations.

I think we have to remember that it takes time build the community to have the conversation and that it doesn’t happen right away. You have to be ready as conversation facilitator. Alexandra Samuel did a workshop called “Bringing Your Community to Life” at Netsquared and offered some terrific practical advice about you get the conversation started.

Some key points:

Key points to encourage participation:

Focus on promoting conversation

Make it happen, don’t wait for it

Connect like-minded participants

Connect complimentary threads

Plan pro-actively, implement reactively

by dbking
Copy Number Variation Detection:
[Via Bench Marks]

With the sequencing of the human genome came the startling revelation that the number of copies of a given gene can vary widely between individuals. This Copy Number Variation (or CNV), contributes to our species’ genetic diversity but it has also been linked to genetic diseases. This month’s issue of Cold Spring Harbor Protocols features a new method for detecting copy number variation. Like all of our monthly featured protocols, it’s freely accessible for subscribers and non-subscribers alike.

Copy Number Variation Detection Via High-Density SNP Genotyping describes the use of PennCNV, a new computational tool for CNV detection in data from genomic arrays. Developed in the laboratory of Maja Bucan at the University of Pennsylvania, the software is freely available for download. Analysis with PennCNV will provide a more comprehensive understanding of genome variation and will aid in studies seeking the causes of genetic diseases. More information on PennCNV can be found in this Genome Research article, PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.

I took the liberty of showing the entire post from David’s blog because, in contrast to my story below, this demonstrates a very good approach for publishing scientific work online.

Protocols, particularly new ones are very useful to have. Making a small number available for free is a nice way to get people to check out the journal. I have it in my newsfeed. I like CSHP and enjoy David’s blog tremendously. Now I just need to find a way to become an adjunct professor at some research organization with an institutional license so I can read all the articles.

Technorati Tags: Open Access, Science, Web 2.0

I posted this at my personal blog but thought it might be of interest here since it demonstrates just how current online tools have changed the way scientific research is published, presented and read.

by Beige Alert
Why snakes don’t have legs:
[Via 2collab public bookmarks]

Tags: Hox gene, Homeobox gene, Limb
Authors: Cunliffe, Vincent
Source: Trends in Genetics; 15, 8, Page 306; 1 August 1999
Sharing: Public

I’m providing a detailed examination of an online journey I took this morning that demonstrates how the Internet has altered the landscape for publishing of articles in scientific journals. Online access certainly changes how we search for and how we read articles. It is also changing where we chose to publish.

So I see this interesting name for an article - Why snakes don’t have legs - in my newsfeed. I click on thru (why it is on 2collab I do not know?) and get this page. Great. ScienceDirect which usually charges for journal access. But this is an article from 1999. Surely it will be open by now?

I went to PubMed, the database of journal articles, and did a search for “snakes AND legs”. Got 48 articles. The critical one appears to be by Cohn and Tickle “Developmental basis of limblessness and axial patterning in snakes” in Nature from June 1999. Great. Now I have a subscription to Nature so this article is available to me but if you wanted to read it without a subscription it would cost $35! Wow! But at least now it has an abstract.

The evolution of snakes involved major changes in vertebrate body plan organization, but the developmental basis of those changes is unknown. The python axial skeleton consists of hundreds of similar vertebrae, forelimbs are absent and hindlimbs are severely reduced. Combined limb loss and trunk elongation is found in many vertebrate taxa1, suggesting that these changes may be linked by a common developmental mechanism. Here we show that Hox gene expression domains are expanded along the body axis in python embryos, and that this can account for both the absence of forelimbs and the expansion of thoracic identity in the axial skeleton. Hindlimb buds are initiated, but apical-ridge and polarizing-region signalling pathways that are normally required for limb development are not activated. Leg bud outgrowth and signalling by Sonic hedgehog in pythons can be rescued by application of fibroblast growth factor or by recombination with chick apical ridge. The failure to activate these signalling pathways during normal python development may also stem from changes in Hox gene expression that occurred early in snake evolution.

Sounds really interesting to me but still not sure it is worth $35. But right above that link from PubMed is another one - from Current Biology with pictures. “How the snake lost its legs”. It is a ScienceDirect link also but this one is available for free. And it has nice pictures while discussing the Cohn and Tickle article.

Except for this nifty one from the Journal of Experimental Biology - “Becoming airborne without legs: the kinematics of take-off in a flying snake, Chrysopelea paradisi” (The picture above is of a flying snake.) Open access and more recently published. Not exactly on topic but it comes with movies! These were just not possible to see without online access. And the movies are really cool and help explain what the author of the paper was describing. You can actually see the difference between a J-loop takeoff and other modes. Plus, flying snakes sound like something from a B-movie.

Back to the topic. I went to Google and searched “Cohn Tickle snake”. The top response is from a USA Today article about why snakes do not have legs. In the article there are links to Martin J. Cohn and Cheryll Tickle. Clicking the Cohn link takes me to his page at the University of Florida. Not a lot here but there is a link to his personal site.

Now we get the Cohn lab page. I could just email him and ask for a copy of the paper (a slightly updated approach to the old method of sending reprint requests by snail mail). But there is a link to Publications.

And here we find the PDF to the paper I was looking for. A quick runthrough reveals that it is a paper I will find interesting (I love Hox stuff). But I would not have paid over $30 for it.

So, for a few minutes of my time I got the article for free and also got to see some nice movies of snakes flying. Not a bad way to travel in an online world.

Technorati Tags: Open Access, Science, Web 2.0

by digitalART (artct45)
A search engine for open notebook science:
[Via Michael Nielsen]

There has been some great discussion in the comments on my post about “Open science”. One outcome is that Jean-Claude Bradley has created a search engine customized for open notebook science:

http://tinyurl.com/4multu

Fittingly, many people contributed to the discussion!

This demonstrates one of the nice abilities of Web 2.0 approaches. Google permits you to set up a custom search for a group of websites. This allows you to perform a directed search using specific terms against a designated group of websites.

A user-generated subset of Google web searches may be very useful for linking the content of several sites. This could be fun to play with. I’ll have to put one together for Science 2.0.

Technorati Tags: Science, Web 2.0

Avogadro: Open Source Molecular Building:
[Via MacResearch - Online Community and Resource for Mac OS X in Science]

Avogadro is a new, open source molecular editor for Mac, Windows, and Linux. It is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

While still in beta, the recent 0.8 release brings general usability to viewing and editing molecules on your Mac. You can quickly export graphics to PNG, JPEG, or even POV-Ray rendering, or copy from the editor and paste a transparent PNG into programs like OmniGraffle. Avogadro supports reading from over 80 chemical file formats, courtesy of the Open Babel library.

read more

These sorts of tools will become more and more common - Open Source, mashable, easy to use. The last paragraph says a lot about the goals.

Future plans for the Mac version of Avogadro include integration of Spotlight and QuickLook, as well as built-in scripting in Python. Work is also underway to allow copy/paste from ChemDraw and other 2D chemical drawing applications. Additional builders (e.g., for biomolecules, nanotubes, and nanoparticles) and interfaces to other computational chemistry packages are due for future versions as well.

Technorati Tags: Social media, Web 2.0